From a7cb0bdf96ad61ce2b044535b2f1e5657875240b Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Thu, 19 Oct 2023 10:36:35 +0200 Subject: [PATCH] feat: implement "seqvars query" command (#201) (#223) --- .gitignore | 2 + Cargo.lock | 333 ++++-- Cargo.toml | 25 +- README.md | 6 + src/common.rs | 2 +- src/main.rs | 4 + src/seqvars/aggregate/mod.rs | 5 +- src/seqvars/ingest/mod.rs | 80 +- ...test__result_snapshot_test@Case_1_vcf.snap | 126 +- ...sult_snapshot_test@NA12878_dragen_vcf.snap | 258 ++-- ...@example_dragen_07_021_624_3_10_4_vcf.snap | 4 +- ...@example_dragen_07_021_624_3_10_9_vcf.snap | 4 +- ...apshot_test@example_gatk_hc_3_7-0_vcf.snap | 4 +- ...shot_test@example_gatk_hc_4_4_0_0_vcf.snap | 4 +- ...ingest__test__result_snapshot_test_gz.snap | 1055 +++++++++-------- src/seqvars/mod.rs | 1 + src/seqvars/query/annonars.rs | 301 +++++ src/seqvars/query/interpreter/clinvar.rs | 50 + src/seqvars/query/interpreter/consequences.rs | 75 ++ src/seqvars/query/interpreter/frequency.rs | 469 ++++++++ .../query/interpreter/genes_allowlist.rs | 94 ++ src/seqvars/query/interpreter/genotype.rs | 647 ++++++++++ src/seqvars/query/interpreter/mod.rs | 81 ++ src/seqvars/query/interpreter/quality.rs | 501 ++++++++ .../query/interpreter/regions_allowlist.rs | 85 ++ src/seqvars/query/mod.rs | 677 +++++++++++ src/seqvars/query/output/call_related.rs | 50 + src/seqvars/query/output/gene_related.rs | 151 +++ src/seqvars/query/output/mod.rs | 52 + src/seqvars/query/output/variant_related.rs | 488 ++++++++ src/seqvars/query/schema.rs | 664 +++++++++++ ...riant_from_vcf@Case_1.ingested.vcf-10.snap | 153 +++ ...riant_from_vcf@Case_1.ingested.vcf-11.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-12.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-13.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-14.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-15.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-16.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-17.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-18.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-19.snap | 44 + ...ariant_from_vcf@Case_1.ingested.vcf-2.snap | 152 +++ ...riant_from_vcf@Case_1.ingested.vcf-20.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-21.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-22.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-23.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-24.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-25.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-26.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-27.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-28.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-29.snap | 44 + ...ariant_from_vcf@Case_1.ingested.vcf-3.snap | 152 +++ ...riant_from_vcf@Case_1.ingested.vcf-30.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-31.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-32.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-33.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-34.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-35.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-36.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-37.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-38.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-39.snap | 44 + ...ariant_from_vcf@Case_1.ingested.vcf-4.snap | 152 +++ ...riant_from_vcf@Case_1.ingested.vcf-40.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-41.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-42.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-43.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-44.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-45.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-46.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-47.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-48.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-49.snap | 44 + ...ariant_from_vcf@Case_1.ingested.vcf-5.snap | 152 +++ ...riant_from_vcf@Case_1.ingested.vcf-50.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-51.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-52.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-53.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-54.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-55.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-56.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-57.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-58.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-59.snap | 44 + ...ariant_from_vcf@Case_1.ingested.vcf-6.snap | 152 +++ ...riant_from_vcf@Case_1.ingested.vcf-60.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-61.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-62.snap | 44 + ...riant_from_vcf@Case_1.ingested.vcf-63.snap | 44 + ...ariant_from_vcf@Case_1.ingested.vcf-7.snap | 152 +++ ...ariant_from_vcf@Case_1.ingested.vcf-8.snap | 152 +++ ...ariant_from_vcf@Case_1.ingested.vcf-9.snap | 152 +++ ..._variant_from_vcf@Case_1.ingested.vcf.snap | 164 +++ ...ariant_from_vcf@dragen.ingested.vcf-2.snap | 32 + ..._variant_from_vcf@dragen.ingested.vcf.snap | 140 +++ ...ema__test__smoke_test_load@empty.json.snap | 90 ++ ...hema__test__smoke_test_load@full.json.snap | 99 ++ ...test__smoke_test_load@with_extra.json.snap | 99 ++ ..._test__smoke_test@Case_1.ingested.vcf.snap | 65 + ..._test__smoke_test@dragen.ingested.vcf.snap | 8 + src/seqvars/query/sorting.rs | 79 ++ src/strucvars/aggregate/cli.rs | 19 +- src/strucvars/ingest/mod.rs | 2 +- src/strucvars/query/interpreter.rs | 6 +- src/strucvars/query/mod.rs | 90 +- src/strucvars/query/schema.rs | 2 +- src/strucvars/txt_to_bin/clinvar/input.rs | 2 +- tests/seqvars/ingest/db/bootstrap.sh | 10 +- .../grch37/seqvars/clinvar/rocksdb/000014.sst | 3 - .../grch37/seqvars/clinvar/rocksdb/000016.sst | 3 - .../grch37/seqvars/clinvar/rocksdb/000036.sst | 3 + .../grch37/seqvars/clinvar/rocksdb/000038.sst | 3 + .../db/grch37/seqvars/clinvar/rocksdb/CURRENT | 2 +- .../db/grch37/seqvars/clinvar/rocksdb/LOG | 4 +- .../clinvar/rocksdb/LOG.old.1697703073190288 | 3 + .../clinvar/rocksdb/LOG.old.1697703223234989 | 3 + .../seqvars/clinvar/rocksdb/MANIFEST-000005 | 3 - .../seqvars/clinvar/rocksdb/MANIFEST-000031 | 3 + .../{OPTIONS-000009 => OPTIONS-000022} | 0 .../{OPTIONS-000011 => OPTIONS-000033} | 0 .../db/grch37/seqvars/clinvar/spec.yaml | 2 +- .../grch37/seqvars/freqs/rocksdb/000018.sst | 3 - .../grch37/seqvars/freqs/rocksdb/000020.sst | 3 - .../grch37/seqvars/freqs/rocksdb/000040.sst | 3 + .../grch37/seqvars/freqs/rocksdb/000042.sst | 3 + .../db/grch37/seqvars/freqs/rocksdb/CURRENT | 2 +- .../db/grch37/seqvars/freqs/rocksdb/LOG | 4 +- .../freqs/rocksdb/LOG.old.1697703073548900 | 3 + .../freqs/rocksdb/LOG.old.1697703223783259 | 3 + .../seqvars/freqs/rocksdb/MANIFEST-000005 | 3 - .../seqvars/freqs/rocksdb/MANIFEST-000035 | 3 + .../{OPTIONS-000013 => OPTIONS-000026} | 0 .../{OPTIONS-000015 => OPTIONS-000037} | 0 tests/seqvars/ingest/db/grch37/txs.bin.zst | 4 +- tests/seqvars/query/Case_1.ingested.vcf | 118 ++ tests/seqvars/query/Case_1.query.json | 121 ++ tests/seqvars/query/Case_1.query.json.bak | 121 ++ tests/seqvars/query/db | 1 + tests/seqvars/query/dragen.ingested.vcf | 53 + tests/seqvars/query/dragen.query.json | 101 ++ tests/seqvars/query/empty.json | 1 + tests/seqvars/query/full.json | 85 ++ tests/seqvars/query/with_extra.json | 86 ++ tests/strucvars/query/bootstrap.sh | 23 + .../db/annonars/genes/rocksdb/000014.sst | 3 + .../db/annonars/genes/rocksdb/000016.sst | 3 + .../query/db/annonars/genes/rocksdb/CURRENT | 3 + .../query/db/annonars/genes/rocksdb/IDENTITY | 3 + .../query/db/annonars/genes/rocksdb/LOCK | 0 .../query/db/annonars/genes/rocksdb/LOG | 3 + .../db/annonars/genes/rocksdb/MANIFEST-000005 | 3 + .../db/annonars/genes/rocksdb/OPTIONS-000009 | 3 + .../db/annonars/genes/rocksdb/OPTIONS-000011 | 3 + .../query/db/annonars/genes/spec.yaml | 3 + .../cadd-grch37-1.6+0.19.0/rocksdb/000014.sst | 3 + .../cadd-grch37-1.6+0.19.0/rocksdb/000016.sst | 3 + .../cadd-grch37-1.6+0.19.0/rocksdb/CURRENT | 3 + .../cadd-grch37-1.6+0.19.0/rocksdb/IDENTITY | 3 + .../cadd/cadd-grch37-1.6+0.19.0/rocksdb/LOCK | 0 .../cadd/cadd-grch37-1.6+0.19.0/rocksdb/LOG | 3 + .../rocksdb/MANIFEST-000005 | 3 + .../rocksdb/OPTIONS-000009 | 3 + .../rocksdb/OPTIONS-000011 | 3 + .../annonars/grch37/cadd/rocksdb/000014.sst | 3 + .../annonars/grch37/cadd/rocksdb/000016.sst | 3 + .../db/annonars/grch37/cadd/rocksdb/CURRENT | 3 + .../db/annonars/grch37/cadd/rocksdb/IDENTITY | 3 + .../db/annonars/grch37/cadd/rocksdb/LOCK | 0 .../query/db/annonars/grch37/cadd/rocksdb/LOG | 3 + .../grch37/cadd/rocksdb/MANIFEST-000005 | 3 + .../grch37/cadd/rocksdb/OPTIONS-000009 | 3 + .../grch37/cadd/rocksdb/OPTIONS-000011 | 3 + .../grch37/clinvar-minimal/rocksdb/000014.sst | 3 + .../grch37/clinvar-minimal/rocksdb/000016.sst | 3 + .../grch37/clinvar-minimal/rocksdb/CURRENT | 3 + .../grch37/clinvar-minimal/rocksdb/IDENTITY | 3 + .../grch37/clinvar-minimal/rocksdb/LOCK | 0 .../grch37/clinvar-minimal/rocksdb/LOG | 3 + .../clinvar-minimal/rocksdb/MANIFEST-000005 | 3 + .../clinvar-minimal/rocksdb/OPTIONS-000009 | 3 + .../clinvar-minimal/rocksdb/OPTIONS-000011 | 3 + .../annonars/grch37/clinvar-minimal/spec.yaml | 3 + .../rocksdb/000014.sst | 3 + .../rocksdb/000016.sst | 3 + .../rocksdb/CURRENT | 3 + .../rocksdb/IDENTITY | 3 + .../cons-grch37-20161007+0.19.0/rocksdb/LOCK | 0 .../cons-grch37-20161007+0.19.0/rocksdb/LOG | 3 + .../rocksdb/MANIFEST-000005 | 3 + .../rocksdb/OPTIONS-000009 | 3 + .../rocksdb/OPTIONS-000011 | 3 + .../annonars/grch37/cons/rocksdb/000014.sst | 3 + .../annonars/grch37/cons/rocksdb/000016.sst | 3 + .../db/annonars/grch37/cons/rocksdb/CURRENT | 3 + .../db/annonars/grch37/cons/rocksdb/IDENTITY | 3 + .../db/annonars/grch37/cons/rocksdb/LOCK | 0 .../query/db/annonars/grch37/cons/rocksdb/LOG | 3 + .../grch37/cons/rocksdb/MANIFEST-000005 | 3 + .../grch37/cons/rocksdb/OPTIONS-000009 | 3 + .../grch37/cons/rocksdb/OPTIONS-000011 | 3 + .../rocksdb/000016.sst | 3 + .../rocksdb/000018.sst | 3 + .../dbnsfp-grch37-4.4a+0.19.0/rocksdb/CURRENT | 3 + .../rocksdb/IDENTITY | 3 + .../dbnsfp-grch37-4.4a+0.19.0/rocksdb/LOCK | 0 .../dbnsfp-grch37-4.4a+0.19.0/rocksdb/LOG | 3 + .../rocksdb/MANIFEST-000005 | 3 + .../rocksdb/OPTIONS-000009 | 3 + .../rocksdb/OPTIONS-000011 | 3 + .../annonars/grch37/dbnsfp/rocksdb/000016.sst | 3 + .../annonars/grch37/dbnsfp/rocksdb/000018.sst | 3 + .../db/annonars/grch37/dbnsfp/rocksdb/CURRENT | 3 + .../annonars/grch37/dbnsfp/rocksdb/IDENTITY | 3 + .../db/annonars/grch37/dbnsfp/rocksdb/LOCK | 0 .../db/annonars/grch37/dbnsfp/rocksdb/LOG | 3 + .../grch37/dbnsfp/rocksdb/MANIFEST-000005 | 3 + .../grch37/dbnsfp/rocksdb/OPTIONS-000009 | 3 + .../grch37/dbnsfp/rocksdb/OPTIONS-000011 | 3 + .../rocksdb/000014.sst | 3 + .../rocksdb/000016.sst | 3 + .../dbscsnv-grch37-1.1+0.19.0/rocksdb/CURRENT | 3 + .../rocksdb/IDENTITY | 3 + .../dbscsnv-grch37-1.1+0.19.0/rocksdb/LOCK | 0 .../dbscsnv-grch37-1.1+0.19.0/rocksdb/LOG | 3 + .../rocksdb/MANIFEST-000005 | 3 + .../rocksdb/OPTIONS-000009 | 3 + .../rocksdb/OPTIONS-000011 | 3 + .../grch37/dbscsnv/rocksdb/000014.sst | 3 + .../grch37/dbscsnv/rocksdb/000016.sst | 3 + .../annonars/grch37/dbscsnv/rocksdb/CURRENT | 3 + .../annonars/grch37/dbscsnv/rocksdb/IDENTITY | 3 + .../db/annonars/grch37/dbscsnv/rocksdb/LOCK | 0 .../db/annonars/grch37/dbscsnv/rocksdb/LOG | 3 + .../grch37/dbscsnv/rocksdb/MANIFEST-000005 | 3 + .../grch37/dbscsnv/rocksdb/OPTIONS-000009 | 3 + .../grch37/dbscsnv/rocksdb/OPTIONS-000011 | 3 + .../rocksdb/000014.sst | 3 + .../rocksdb/000016.sst | 3 + .../dbsnp-grch37-b151+0.19.0/rocksdb/CURRENT | 3 + .../dbsnp-grch37-b151+0.19.0/rocksdb/IDENTITY | 3 + .../dbsnp-grch37-b151+0.19.0/rocksdb/LOCK | 0 .../dbsnp-grch37-b151+0.19.0/rocksdb/LOG | 3 + .../rocksdb/MANIFEST-000005 | 3 + .../rocksdb/OPTIONS-000009 | 3 + .../rocksdb/OPTIONS-000011 | 3 + .../annonars/grch37/dbsnp/rocksdb/000014.sst | 3 + .../annonars/grch37/dbsnp/rocksdb/000016.sst | 3 + .../db/annonars/grch37/dbsnp/rocksdb/CURRENT | 3 + .../db/annonars/grch37/dbsnp/rocksdb/IDENTITY | 3 + .../db/annonars/grch37/dbsnp/rocksdb/LOCK | 0 .../db/annonars/grch37/dbsnp/rocksdb/LOG | 3 + .../grch37/dbsnp/rocksdb/MANIFEST-000005 | 3 + .../grch37/dbsnp/rocksdb/OPTIONS-000009 | 3 + .../grch37/dbsnp/rocksdb/OPTIONS-000011 | 3 + 255 files changed, 11054 insertions(+), 922 deletions(-) create mode 100644 src/seqvars/query/annonars.rs create mode 100644 src/seqvars/query/interpreter/clinvar.rs create mode 100644 src/seqvars/query/interpreter/consequences.rs create mode 100644 src/seqvars/query/interpreter/frequency.rs create mode 100644 src/seqvars/query/interpreter/genes_allowlist.rs create mode 100644 src/seqvars/query/interpreter/genotype.rs create mode 100644 src/seqvars/query/interpreter/mod.rs create mode 100644 src/seqvars/query/interpreter/quality.rs create mode 100644 src/seqvars/query/interpreter/regions_allowlist.rs create mode 100644 src/seqvars/query/mod.rs create mode 100644 src/seqvars/query/output/call_related.rs create mode 100644 src/seqvars/query/output/gene_related.rs create mode 100644 src/seqvars/query/output/mod.rs create mode 100644 src/seqvars/query/output/variant_related.rs create mode 100644 src/seqvars/query/schema.rs create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-10.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-11.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-12.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-13.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-14.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-15.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-16.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-17.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-18.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-19.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-2.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-20.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-21.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-22.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-23.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-24.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-25.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-26.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-27.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-28.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-29.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-3.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-30.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-31.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-32.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-33.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-34.snap create mode 100644 src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-35.snap create mode 100644 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create mode 100644 tests/strucvars/query/db/annonars/grch37/dbsnp/rocksdb/OPTIONS-000011 diff --git a/.gitignore b/.gitignore index 8391d9e1..a0dcb48f 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,5 @@ +*.snap.new + /*.json ## Text Editors diff --git a/Cargo.lock b/Cargo.lock index f49aede8..218e0a86 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -31,7 +31,7 @@ dependencies = [ "actix-utils", "ahash", "base64", - "bitflags 2.4.0", + "bitflags 2.4.1", "brotli", "bytes", "bytestring", @@ -210,9 +210,9 @@ dependencies = [ [[package]] name = "aho-corasick" -version = "1.1.1" +version = "1.1.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ea5d730647d4fadd988536d06fecce94b7b4f2a7efdae548f1cf4b63205518ab" +checksum = "b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0" dependencies = [ "memchr", ] @@ -255,9 +255,9 @@ dependencies = [ [[package]] name = "annonars" -version = "0.23.1" +version = "0.24.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "17a6e189155aa6d3488e373db9625fc80733ec50cda565e6ed4b160a337760c8" +checksum = "0058c9550498950a103798c6976abfae6016762c1ac355dd46c9792c533ac50c" dependencies = [ "actix-web", "anyhow", @@ -363,9 +363,9 @@ dependencies = [ [[package]] name = "async-trait" -version = "0.1.73" +version = "0.1.74" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "bc00ceb34980c03614e35a3a4e218276a0a824e911d07651cd0d858a51e8c0f0" +checksum = "a66537f1bb974b254c98ed142ff995236e81b9d0fe4db0575f46612cb15eb0f9" dependencies = [ "proc-macro2", "quote", @@ -514,9 +514,9 @@ checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a" [[package]] name = "bitflags" -version = "2.4.0" +version = "2.4.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "b4682ae6287fcf752ecaabbfcc7b6f9b72aa33933dc23a554d853aea8eea8635" +checksum = "327762f6e5a765692301e5bb513e0d9fef63be86bbc14528052b1cd3e6f03e07" [[package]] name = "block-buffer" @@ -604,6 +604,12 @@ version = "1.5.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "a2bd12c1caf447e69cd4528f47f94d203fd2582878ecb9e9465484c4148a8223" +[[package]] +name = "bytesize" +version = "1.3.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a3e368af43e418a04d52505cf3dbc23dda4e3407ae2fa99fd0e4f308ce546acc" + [[package]] name = "bytestring" version = "1.3.0" @@ -865,14 +871,38 @@ version = "0.1.7" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "ef8ae57c4978a2acd8b869ce6b9ca1dfe817bff704c220209fdef2c0b75a01b9" +[[package]] +name = "darling" +version = "0.14.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7b750cb3417fd1b327431a470f388520309479ab0bf5e323505daf0290cd3850" +dependencies = [ + "darling_core 0.14.4", + "darling_macro 0.14.4", +] + [[package]] name = "darling" version = "0.20.3" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "0209d94da627ab5605dcccf08bb18afa5009cfbef48d8a8b7d7bdbc79be25c5e" dependencies = [ - "darling_core", - "darling_macro", + "darling_core 0.20.3", + "darling_macro 0.20.3", +] + +[[package]] +name = "darling_core" +version = "0.14.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "109c1ca6e6b7f82cc233a97004ea8ed7ca123a9af07a8230878fcfda9b158bf0" +dependencies = [ + "fnv", + "ident_case", + "proc-macro2", + "quote", + "strsim", + "syn 1.0.109", ] [[package]] @@ -889,23 +919,55 @@ dependencies = [ "syn 2.0.38", ] +[[package]] +name = "darling_macro" +version = "0.14.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a4aab4dbc9f7611d8b55048a3a16d2d010c2c8334e46304b40ac1cc14bf3b48e" +dependencies = [ + "darling_core 0.14.4", + "quote", + "syn 1.0.109", +] + [[package]] name = "darling_macro" version = "0.20.3" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "836a9bbc7ad63342d6d6e7b815ccab164bc77a2d95d84bc3117a8c0d5c98e2d5" dependencies = [ - "darling_core", + "darling_core 0.20.3", "quote", "syn 2.0.38", ] +[[package]] +name = "deepsize" +version = "0.2.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1cdb987ec36f6bf7bfbea3f928b75590b736fc42af8e54d97592481351b2b96c" +dependencies = [ + "deepsize_derive", +] + +[[package]] +name = "deepsize_derive" +version = "0.1.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "990101d41f3bc8c1a45641024377ee284ecc338e5ecf3ea0f0e236d897c72796" +dependencies = [ + "proc-macro2", + "quote", + "syn 1.0.109", +] + [[package]] name = "deranged" -version = "0.3.8" +version = "0.3.9" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f2696e8a945f658fd14dc3b87242e6b80cd0f36ff04ea560fa39082368847946" +checksum = "0f32d04922c60427da6f9fef14d042d9edddef64cb9d4ce0d64d0685fbeb1fd3" dependencies = [ + "powerfmt", "serde", ] @@ -931,6 +993,37 @@ dependencies = [ "syn 1.0.109", ] +[[package]] +name = "derive_builder" +version = "0.12.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "8d67778784b508018359cbc8696edb3db78160bab2c2a28ba7f56ef6932997f8" +dependencies = [ + "derive_builder_macro", +] + +[[package]] +name = "derive_builder_core" +version = "0.12.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "c11bdc11a0c47bc7d37d582b5285da6849c96681023680b906673c5707af7b0f" +dependencies = [ + "darling 0.14.4", + "proc-macro2", + "quote", + "syn 1.0.109", +] + +[[package]] +name = "derive_builder_macro" +version = "0.12.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ebcda35c7a396850a55ffeac740804b40ffec779b98fffbb1738f4033f0ee79e" +dependencies = [ + "derive_builder_core", + "syn 1.0.109", +] + [[package]] name = "derive_more" version = "0.99.17" @@ -1071,23 +1164,27 @@ checksum = "5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5" [[package]] name = "errno" -version = "0.3.4" +version = "0.3.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "add4f07d43996f76ef320709726a556a9d4f965d9410d8d0271132d2f8293480" +checksum = "ac3e13f66a2f95e32a39eaa81f6b95d42878ca0e1db0c7543723dfe12557e860" dependencies = [ - "errno-dragonfly", "libc", "windows-sys 0.48.0", ] [[package]] -name = "errno-dragonfly" -version = "0.1.2" +name = "ext-sort" +version = "0.1.4" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "aa68f1b12764fab894d2755d2518754e71b4fd80ecfb822714a1206c2aab39bf" +checksum = "fcf73e44617eab501beba39234441a194cf138629d3b6447f81f573e1c3d0a13" dependencies = [ - "cc", - "libc", + "bytesize", + "deepsize", + "log", + "rayon", + "rmp-serde", + "serde", + "tempfile", ] [[package]] @@ -1134,9 +1231,9 @@ checksum = "0ce7134b9999ecaf8bcd65542e436736ef32ddca1b3e06094cb6ec5755203b80" [[package]] name = "flate2" -version = "1.0.27" +version = "1.0.28" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c6c98ee8095e9d1dcbf2fcc6d95acccb90d1c81db1e44725c6a984b1dbdfb010" +checksum = "46303f565772937ffe1d394a4fac6f411c6013172fadde9dcdb1e147a086940e" dependencies = [ "crc32fast", "miniz_oxide", @@ -1464,16 +1561,16 @@ checksum = "a17b27f28a7466846baca75f0a5244e546e44178eb7f1c07a3820f413e91c6b0" [[package]] name = "iana-time-zone" -version = "0.1.57" +version = "0.1.58" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2fad5b825842d2b38bd206f3e81d6957625fd7f0a361e345c30e01a0ae2dd613" +checksum = "8326b86b6cff230b97d0d312a6c40a60726df3332e721f72a1b035f451663b20" dependencies = [ "android_system_properties", "core-foundation-sys", "iana-time-zone-haiku", "js-sys", "wasm-bindgen", - "windows", + "windows-core", ] [[package]] @@ -1578,7 +1675,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "cb0889898416213fab133e1d33a0e5858a48177452750691bde3666d0fdbaf8b" dependencies = [ "hermit-abi", - "rustix 0.38.17", + "rustix 0.38.19", "windows-sys 0.48.0", ] @@ -1608,9 +1705,9 @@ checksum = "af150ab688ff2122fcef229be89cb50dd66af9e01a4ff320cc137eecc9bacc38" [[package]] name = "jobserver" -version = "0.1.26" +version = "0.1.27" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "936cfd212a0155903bcbc060e316fb6cc7cbf2e1907329391ebadc1fe0ce77c2" +checksum = "8c37f63953c4c63420ed5fd3d6d398c719489b9f872b9fa683262f8edd363c7d" dependencies = [ "libc", ] @@ -1655,9 +1752,9 @@ checksum = "830d08ce1d1d941e6b30645f1a0eb5643013d835ce3779a5fc208261dbe10f55" [[package]] name = "libc" -version = "0.2.148" +version = "0.2.149" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "9cdc71e17332e86d2e1d38c1f99edcb6288ee11b815fb1a4b049eaa2114d369b" +checksum = "a08173bc88b7955d1b3145aa561539096c421ac8debde8cbc3612ec635fee29b" [[package]] name = "libloading" @@ -1726,9 +1823,9 @@ checksum = "f051f77a7c8e6957c0696eac88f26b0117e54f52d3fc682ab19397a8812846a4" [[package]] name = "linux-raw-sys" -version = "0.4.8" +version = "0.4.10" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "3852614a3bd9ca9804678ba6be5e3b8ce76dfc902cae004e3e0c44051b6e88db" +checksum = "da2479e8c062e40bf0066ffa0bc823de0a9368974af99c9f6df941d2c231e03f" [[package]] name = "local-channel" @@ -1749,9 +1846,9 @@ checksum = "e34f76eb3611940e0e7d53a9aaa4e6a3151f69541a282fd0dad5571420c53ff1" [[package]] name = "lock_api" -version = "0.4.10" +version = "0.4.11" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c1cc9717a20b1bb222f333e6a92fd32f7d8a18ddc5a3191a11af45dcbf4dcd16" +checksum = "3c168f8615b12bc01f9c17e2eb0cc07dcae1940121185446edc3744920e8ef45" dependencies = [ "autocfg", "scopeguard", @@ -1804,9 +1901,9 @@ dependencies = [ [[package]] name = "mehari" -version = "0.13.0" +version = "0.14.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ad5a7d9e2c5c19a95ec03a385a867b30d66cc7237f916f3ff0071ab7eb990f0d" +checksum = "6f7d28d45b0c27d227b832b059ef52e2f8a30d03087369b21b734216f3710197" dependencies = [ "actix-web", "annonars", @@ -2130,9 +2227,9 @@ dependencies = [ [[package]] name = "num-traits" -version = "0.2.16" +version = "0.2.17" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f30b0abd723be7e2ffca1272140fac1a2f084c77ec3e123c192b66af1ee9e6c2" +checksum = "39e3200413f237f41ab11ad6d161bc7239c84dcb631773ccd7de3dfe4b5c267c" dependencies = [ "autocfg", "libm", @@ -2167,9 +2264,9 @@ checksum = "04744f49eae99ab78e0d5c0b603ab218f515ea8cfe5a456d7629ad883a3b6e7d" [[package]] name = "ordered-float" -version = "3.9.1" +version = "3.9.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2a54938017eacd63036332b4ae5c8a49fc8c0c1d6d629893057e4f13609edd06" +checksum = "f1e1c390732d15f1d48471625cd92d154e66db2c56645e29a9cd26f4699f72dc" dependencies = [ "num-traits", ] @@ -2192,13 +2289,13 @@ dependencies = [ [[package]] name = "parking_lot_core" -version = "0.9.8" +version = "0.9.9" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "93f00c865fe7cabf650081affecd3871070f26767e7b2070a3ffae14c654b447" +checksum = "4c42a9226546d68acdd9c0a280d17ce19bfe27a46bf68784e4066115788d008e" dependencies = [ "cfg-if", "libc", - "redox_syscall 0.3.5", + "redox_syscall 0.4.1", "smallvec", "windows-targets 0.48.5", ] @@ -2343,6 +2440,12 @@ dependencies = [ "postgres-protocol", ] +[[package]] +name = "powerfmt" +version = "0.2.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "439ee305def115ba05938db6eb1644ff94165c5ab5e9420d1c1bcedbba909391" + [[package]] name = "ppv-lite86" version = "0.2.17" @@ -2395,9 +2498,9 @@ dependencies = [ [[package]] name = "proc-macro2" -version = "1.0.68" +version = "1.0.69" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5b1106fec09662ec6dd98ccac0f81cef56984d0b49f75c92d8cbad76e20c005c" +checksum = "134c189feb4956b20f6f547d2cf727d4c0fe06722b20a0eec87ed445a97f92da" dependencies = [ "unicode-ident", ] @@ -2414,7 +2517,7 @@ dependencies = [ "flate2", "hex", "lazy_static", - "rustix 0.36.15", + "rustix 0.36.16", ] [[package]] @@ -2613,6 +2716,15 @@ dependencies = [ "bitflags 1.3.2", ] +[[package]] +name = "redox_syscall" +version = "0.4.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "4722d768eff46b75989dd134e5c353f0d6296e5aaa3132e776cbdb56be7731aa" +dependencies = [ + "bitflags 1.3.2", +] + [[package]] name = "redox_users" version = "0.4.3" @@ -2626,13 +2738,13 @@ dependencies = [ [[package]] name = "regex" -version = "1.10.1" +version = "1.10.2" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "aaac441002f822bc9705a681810a4dd2963094b9ca0ddc41cb963a4c189189ea" +checksum = "380b951a9c5e80ddfd6136919eef32310721aa4aacd4889a8d39124b026ab343" dependencies = [ "aho-corasick", "memchr", - "regex-automata 0.4.2", + "regex-automata 0.4.3", "regex-syntax 0.8.2", ] @@ -2647,9 +2759,9 @@ dependencies = [ [[package]] name = "regex-automata" -version = "0.4.2" +version = "0.4.3" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5011c7e263a695dc8ca064cddb722af1be54e517a280b12a5356f98366899e5d" +checksum = "5f804c7828047e88b2d32e2d7fe5a105da8ee3264f01902f796c8e067dc2483f" dependencies = [ "aho-corasick", "memchr", @@ -2689,6 +2801,28 @@ dependencies = [ "winapi", ] +[[package]] +name = "rmp" +version = "0.8.12" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7f9860a6cc38ed1da53456442089b4dfa35e7cedaa326df63017af88385e6b20" +dependencies = [ + "byteorder", + "num-traits", + "paste", +] + +[[package]] +name = "rmp-serde" +version = "1.1.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "bffea85eea980d8a74453e5d02a8d93028f3c34725de143085a844ebe953258a" +dependencies = [ + "byteorder", + "rmp", + "serde", +] + [[package]] name = "rocksdb" version = "0.21.0" @@ -2745,7 +2879,7 @@ version = "0.29.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "549b9d036d571d42e6e85d1c1425e2ac83491075078ca9a15be021c56b1641f2" dependencies = [ - "bitflags 2.4.0", + "bitflags 2.4.1", "fallible-iterator", "fallible-streaming-iterator", "hashlink", @@ -2780,14 +2914,14 @@ version = "0.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "bfa0f585226d2e68097d4f95d113b15b83a82e819ab25717ec0590d9584ef366" dependencies = [ - "semver 1.0.19", + "semver 1.0.20", ] [[package]] name = "rustix" -version = "0.36.15" +version = "0.36.16" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "c37f1bd5ef1b5422177b7646cba67430579cfe2ace80f284fee876bca52ad941" +checksum = "6da3636faa25820d8648e0e31c5d519bbb01f72fdf57131f0f5f7da5fed36eab" dependencies = [ "bitflags 1.3.2", "errno", @@ -2799,14 +2933,14 @@ dependencies = [ [[package]] name = "rustix" -version = "0.38.17" +version = "0.38.19" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "f25469e9ae0f3d0047ca8b93fc56843f38e6774f0914a107ff8b41be8be8e0b7" +checksum = "745ecfa778e66b2b63c88a61cb36e0eea109e803b0b86bf9879fbc77c70e86ed" dependencies = [ - "bitflags 2.4.0", + "bitflags 2.4.1", "errno", "libc", - "linux-raw-sys 0.4.8", + "linux-raw-sys 0.4.10", "windows-sys 0.48.0", ] @@ -2845,9 +2979,9 @@ checksum = "d4f410fedcf71af0345d7607d246e7ad15faaadd49d240ee3b24e5dc21a820ac" [[package]] name = "semver" -version = "1.0.19" +version = "1.0.20" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ad977052201c6de01a8ef2aa3378c4bd23217a056337d1d6da40468d267a4fb0" +checksum = "836fa6a3e1e547f9a2c4040802ec865b5d85f4014efe00555d7090a3dcaa1090" [[package]] name = "seqrepo" @@ -2866,28 +3000,18 @@ dependencies = [ [[package]] name = "serde" -version = "1.0.188" +version = "1.0.189" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "cf9e0fcba69a370eed61bcf2b728575f726b50b55cba78064753d708ddc7549e" +checksum = "8e422a44e74ad4001bdc8eede9a4570ab52f71190e9c076d14369f38b9200537" dependencies = [ "serde_derive", ] -[[package]] -name = "serde-jsonlines" -version = "0.4.0" -source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4684abdec99c1de7e507a3516c82385ff74d54c385973846b079bfd9f5920d35" -dependencies = [ - "serde", - "serde_json", -] - [[package]] name = "serde_derive" -version = "1.0.188" +version = "1.0.189" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "4eca7ac642d82aa35b60049a6eccb4be6be75e599bd2e9adb5f875a737654af2" +checksum = "1e48d1f918009ce3145511378cf68d613e3b3d9137d67272562080d68a2b32d5" dependencies = [ "proc-macro2", "quote", @@ -2929,9 +3053,9 @@ dependencies = [ [[package]] name = "serde_with" -version = "3.3.0" +version = "3.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "1ca3b16a3d82c4088f343b7480a93550b3eabe1a358569c2dfe38bbcead07237" +checksum = "64cd236ccc1b7a29e7e2739f27c0b2dd199804abc4290e32f59f3b68d6405c23" dependencies = [ "base64", "chrono", @@ -2946,11 +3070,11 @@ dependencies = [ [[package]] name = "serde_with_macros" -version = "3.3.0" +version = "3.4.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "2e6be15c453eb305019bfa438b1593c731f36a289a7853f7707ee29e870b3b3c" +checksum = "93634eb5f75a2323b16de4748022ac4297f9e76b6dced2be287a099f41b5e788" dependencies = [ - "darling", + "darling 0.20.3", "proc-macro2", "quote", "syn 2.0.38", @@ -3026,9 +3150,9 @@ dependencies = [ [[package]] name = "similar" -version = "2.2.1" +version = "2.3.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "420acb44afdae038210c99e69aae24109f32f15500aa708e81d46c9f29d55fcf" +checksum = "2aeaf503862c419d66959f5d7ca015337d864e9c49485d771b732e2a20453597" [[package]] name = "siphasher" @@ -3189,7 +3313,7 @@ dependencies = [ "cfg-if", "fastrand", "redox_syscall 0.3.5", - "rustix 0.38.17", + "rustix 0.38.19", "windows-sys 0.48.0", ] @@ -3240,12 +3364,13 @@ dependencies = [ [[package]] name = "time" -version = "0.3.29" +version = "0.3.30" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "426f806f4089c493dcac0d24c29c01e2c38baf8e30f1b716ee37e83d200b18fe" +checksum = "c4a34ab300f2dee6e562c10a046fc05e358b29f9bf92277f30c3c8d82275f6f5" dependencies = [ "deranged", "itoa", + "powerfmt", "serde", "time-core", "time-macros", @@ -3283,9 +3408,9 @@ checksum = "1f3ccbac311fea05f86f61904b462b55fb3df8837a366dfc601a0161d0532f20" [[package]] name = "tokio" -version = "1.32.0" +version = "1.33.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "17ed6077ed6cd6c74735e21f37eb16dc3935f96878b1fe961074089cc80893f9" +checksum = "4f38200e3ef7995e5ef13baec2f432a6da0aa9ac495b2c0e8f3b7eec2c92d653" dependencies = [ "backtrace", "bytes", @@ -3340,9 +3465,9 @@ dependencies = [ [[package]] name = "tracing" -version = "0.1.39" +version = "0.1.40" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ee2ef2af84856a50c1d430afce2fdded0a4ec7eda868db86409b4543df0797f9" +checksum = "c3523ab5a71916ccf420eebdf5521fcef02141234bbc0b8a49f2fdc4544364ef" dependencies = [ "log", "pin-project-lite", @@ -3487,9 +3612,9 @@ checksum = "711b9620af191e0cdc7468a8d14e709c3dcdb115b36f838e601583af800a370a" [[package]] name = "uuid" -version = "1.4.1" +version = "1.5.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "79daa5ed5740825c40b389c5e50312b9c86df53fccd33f281df655642b43869d" +checksum = "88ad59a7560b41a70d191093a945f0b87bc1deeda46fb237479708a1d6b6cdfc" dependencies = [ "getrandom", "rand 0.8.5", @@ -3512,12 +3637,16 @@ dependencies = [ "bio", "byte-unit", "byteorder", + "bytesize", "chrono", "clap", "clap-verbosity-flag", "console", "csv", + "derive-new", + "derive_builder", "enum-map 2.6.3", + "ext-sort", "fastrand", "file_diff", "flate2", @@ -3544,7 +3673,6 @@ dependencies = [ "rocksdb-utils-lookup", "rstest", "serde", - "serde-jsonlines", "serde_json", "serde_test", "serde_with", @@ -3661,7 +3789,7 @@ dependencies = [ "either", "home", "once_cell", - "rustix 0.38.17", + "rustix 0.38.19", ] [[package]] @@ -3676,9 +3804,9 @@ dependencies = [ [[package]] name = "wide" -version = "0.7.12" +version = "0.7.13" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "ebecebefc38ff1860b4bc47550bbfa63af5746061cf0d29fcd7fa63171602598" +checksum = "c68938b57b33da363195412cfc5fc37c9ed49aa9cfe2156fde64b8d2c9498242" dependencies = [ "bytemuck", "safe_arch", @@ -3716,10 +3844,10 @@ source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f" [[package]] -name = "windows" -version = "0.48.0" +name = "windows-core" +version = "0.51.1" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "e686886bc078bc1b0b600cac0147aadb815089b6e4da64016cbd754b6342700f" +checksum = "f1f8cf84f35d2db49a46868f947758c7a1138116f7fac3bc844f43ade1292e64" dependencies = [ "windows-targets 0.48.5", ] @@ -3910,11 +4038,10 @@ dependencies = [ [[package]] name = "zstd-sys" -version = "2.0.8+zstd.1.5.5" +version = "2.0.9+zstd.1.5.5" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "5556e6ee25d32df2586c098bbfa278803692a20d0ab9565e049480d52707ec8c" +checksum = "9e16efa8a874a0481a574084d34cc26fdb3b99627480f785888deb6386506656" dependencies = [ "cc", - "libc", "pkg-config", ] diff --git a/Cargo.toml b/Cargo.toml index 51200dd9..252c5280 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -12,30 +12,41 @@ rust-version = "1.64.0" # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html [dependencies] -annonars = "0.23" +annonars = "0.24" anyhow = { version = "1.0", features = ["backtrace"] } base16ct = "0.2" bio = "1.4" +byteorder = { version = "1.5", features = ["i128"] } +bytesize = "1.3" byte-unit = "4.0" chrono = { version = "0.4", features = ["serde"] } clap-verbosity-flag = "2.0" clap = { version = "4.4", features = ["derive", "help"] } console = "0.15" csv = "1.1" +derive_builder = { version = "0.12", features = ["clippy"] } +derive-new = "0.5.9" enum-map = { version = "2.6", features = ["serde"] } +ext-sort = { version = "0.1", features = ["memory-limit", "bytesize"] } fastrand = "2.0" flate2 = "1.0" hgvs = "0.11" indexmap = { version = "2.0", features = ["serde"] } itertools = "0.11" log = "0.4" -mehari = "0.13" +mehari = "0.14" multimap = "0.9" +noodles-bgzf = "0.25" +noodles-vcf = "0.41" procfs = "0.15" prost = "0.12" +rand = "0.8" +rand_core = "0.6" +rayon = "1.8" regex = "1.10" +rocksdb-utils-lookup = "0.3" +rocksdb = { version = "0.21", features = ["multi-threaded-cf"] } serde_json = "1.0" -serde-jsonlines = "0.4" serde = { version = "1.0", features = ["serde_derive"] } serde_with = { version = "3.3", features = ["indexmap_2"] } shellexpand = "3.0" @@ -47,14 +58,6 @@ thousands = "0.2" tracing = "0.1" tracing-subscriber = "0.3" uuid = { version = "1.4", features = ["v4", "fast-rng", "serde"] } -noodles-vcf = "0.41.0" -rocksdb = { version = "0.21.0", features = ["multi-threaded-cf"] } -noodles-bgzf = "0.25.0" -rand = "0.8" -rand_core = "0.6" -rocksdb-utils-lookup = "0.3.0" -rayon = "1.8.0" -byteorder = { version = "1.5.0", features = ["i128"] } [build-dependencies] prost-build = "0.12" diff --git a/README.md b/README.md index 568f3a1d..a1c3af05 100644 --- a/README.md +++ b/README.md @@ -45,6 +45,8 @@ This command takes as the input a single VCF file from a (supported) variant cal The command interprets the following fields which are written out by the commonly used variant callers such as GATK UnifiedGenotyper, GATK HaplotypeCaller, and Illumina Dragen. - `FORMAT/GT` -- genotype + - the following `GT` values are written out as `0/0`, `0/1`, `1/0`, `1/1`, `0|0`, `0|1`, `1|0`, `1|1`, `./.`, `.|.`, `.` + - no combination of no-call (`.`) and called allele is written out - `FORMAT/GQ` -- genotype quality - `FORMAT/DP` -- total read coverage - `FORMAT/AD` -- allelic depth, one value per allele (including reference0) @@ -144,6 +146,10 @@ varfish-server-worker seqvars aggregate \ --path-in-vcf @path/to/file/list.txt ``` +## The `seqvars query` Command + +This command perform the querying of sequence variants and further annotation using annonars databases. + ## The `strucvars ingest` Command This command takes as the input one or more VCF files from structural variant callers and converts it into a file for further querying. diff --git a/src/common.rs b/src/common.rs index c33e798f..423c1523 100644 --- a/src/common.rs +++ b/src/common.rs @@ -199,7 +199,7 @@ impl std::str::FromStr for GenomeRelease { } /// Helper type for encoding genotypes in parsing. -#[derive(Copy, Clone)] +#[derive(Copy, Clone, Debug, PartialEq, Eq)] pub enum Genotype { /// hom. ref. HomRef, diff --git a/src/main.rs b/src/main.rs index 4ca2bca2..666fc83d 100644 --- a/src/main.rs +++ b/src/main.rs @@ -68,6 +68,7 @@ enum SeqvarsCommands { Aggregate(seqvars::aggregate::Args), Ingest(seqvars::ingest::Args), Prefilter(seqvars::prefilter::Args), + Query(seqvars::query::Args), } fn main() -> Result<(), anyhow::Error> { @@ -103,6 +104,9 @@ fn main() -> Result<(), anyhow::Error> { SeqvarsCommands::Prefilter(args) => { seqvars::prefilter::run(&cli.common, args)?; } + SeqvarsCommands::Query(args) => { + seqvars::query::run(&cli.common, args)?; + } }, Commands::Strucvars(strucvars) => match &strucvars.command { StrucvarsCommands::Aggregate(args) => { diff --git a/src/seqvars/aggregate/mod.rs b/src/seqvars/aggregate/mod.rs index a7f5afdc..ee718fc6 100644 --- a/src/seqvars/aggregate/mod.rs +++ b/src/seqvars/aggregate/mod.rs @@ -53,7 +53,6 @@ fn handle_record( let mut res_counts = ds::Counts::default(); let mut res_carriers = ds::CarrierList::default(); - // TODO properly handle PAR regions for (name, sample) in input_header .sample_names() .iter() @@ -165,8 +164,6 @@ fn import_vcf( for input_record in records { let input_record = input_record?; - // TODO: we need to lock the database for counts - // Obtain counts from the current variant. let (this_counts_data, this_carrier_data) = handle_record(&input_record, &input_header, &pedigree, &case_uuid)?; @@ -253,7 +250,7 @@ fn import_vcf( } } - todo!() + Ok(()) } /// Perform the parallel import of VCF files. diff --git a/src/seqvars/ingest/mod.rs b/src/seqvars/ingest/mod.rs index c96158d7..a9524d8d 100644 --- a/src/seqvars/ingest/mod.rs +++ b/src/seqvars/ingest/mod.rs @@ -106,22 +106,87 @@ impl KnownFormatKeys { /// The known `FORMAT` keys. static KNOWN_FORMAT_KEYS: OnceLock = OnceLock::new(); +/// Regular expression for parsing `GT` values. +static GT_RE: OnceLock = OnceLock::new(); + /// Transform the ``FORMAT`` key if known. fn transform_format_value( value: &Option<&vcf::record::genotypes::sample::Value>, key: &vcf::record::genotypes::keys::Key, allele_no: usize, + sample: &vcf::record::genotypes::Sample<'_>, ) -> Option> { + let gt_re = GT_RE + .get_or_init(|| regex::Regex::new(r"([^\|]+)([/|])([^\|]+)").expect("could not parse RE")); + + let curr_allele = format!("{}", allele_no); + + fn transform_allele(allele_to_transform: &str, curr_allele: &str) -> &'static str { + if allele_to_transform == curr_allele { + "1" + } else { + "0" + } + } + if let Some(value) = value { Some(Some(match key.as_ref() { + "GT" => { + let gt = match sample + .get(&vcf::record::genotypes::keys::key::GENOTYPE) + .expect("FORMAT/GT must be present") + .cloned() + .unwrap_or_else(|| unreachable!("FORMAT/GT must be present and not None")) + { + vcf::record::genotypes::sample::Value::String(gt) => gt.clone(), + _ => unreachable!("FORMAT/GT must be string"), + }; + if ["./.", ".|.", "."].contains(>.as_str()) { + // no need to transform no-call + vcf::record::genotypes::sample::Value::String(gt) + } else { + // transform all others + let gt_captures = gt_re + .captures(>) + .unwrap_or_else(|| panic!("FORMAT/GT cannot be parsed: {}", >)); + let gt_1 = gt_captures.get(1).expect("must be capture").as_str(); + let gt_2 = gt_captures.get(2).expect("must be capture").as_str(); + let gt_3 = gt_captures.get(3).expect("must be capture").as_str(); + + let new_gt = format!( + "{}{}{}", + transform_allele(gt_1, &curr_allele), + gt_2, + transform_allele(gt_3, &curr_allele), + ); + + vcf::record::genotypes::sample::Value::String(new_gt) + } + } "AD" => { - // Only write out current allele as AD. + let dp = match sample + .get(&vcf::record::genotypes::keys::key::READ_DEPTH) + .expect("FORMAT/DP must be present") + .cloned() + .unwrap_or_else(|| unreachable!("FORMAT/DP must be present and not None")) + { + vcf::record::genotypes::sample::Value::Integer(dp) => dp, + _ => unreachable!("FORMAT/DP must be integer"), + }; + + // Only write out reference and current allele as AD. match *value { vcf::record::genotypes::sample::Value::Array( vcf::record::genotypes::sample::value::Array::Integer(ad_values), - ) => vcf::record::genotypes::sample::Value::Integer( - ad_values[allele_no].expect("SQ should be integer value"), - ), + ) => { + let ad = ad_values[allele_no].expect("AD should be integer value"); + vcf::record::genotypes::sample::Value::Array( + vcf::record::genotypes::sample::value::Array::Integer(vec![ + Some(dp - ad), + Some(ad), + ]), + ) + } _ => return None, // unreachable!("FORMAT/AD must be array of integer"), } } @@ -134,7 +199,7 @@ fn transform_format_value( vcf::record::genotypes::sample::Value::Array( vcf::record::genotypes::sample::value::Array::Float(sq_values), ) => vcf::record::genotypes::sample::Value::Float( - sq_values[allele_no].expect("SQ should be float value"), + sq_values[allele_no - 1].expect("SQ should be float value"), ), _ => return None, // unreachable!("FORMAT/PS must be integer"), } @@ -181,7 +246,9 @@ fn copy_format( .iter() .map(|key| { let input_value = sample.get(key).expect("key must be valid"); - if let Some(value) = transform_format_value(&input_value, key, allele_no) { + if let Some(value) = + transform_format_value(&input_value, key, allele_no, &sample) + { value } else if known_format_keys.output_keys.contains(key) { input_value.cloned() @@ -290,6 +357,7 @@ where let input_record = input_record?; for (allele_no, alt_allele) in input_record.alternate_bases().iter().enumerate() { + let allele_no = allele_no + 1; // Construct record with first few fields describing one variant allele. let builder = vcf::Record::builder() .set_chromosome(input_record.chromosome().clone()) diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@Case_1_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@Case_1_vcf.snap index 70a28fa3..54eb7651 100644 --- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@Case_1_vcf.snap +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@Case_1_vcf.snap @@ -57,67 +57,67 @@ expression: "std::fs::read_to_string(&args.path_out)?" ##x-varfish-version= ##x-varfish-version= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Case_1_father-N1-DNA1-WGS1 Case_1_index-N1-DNA1-WGS1 Case_1_mother-N1-DNA1-WGS1 -17 41249263 . G A . . gnomad_exomes_an=31398;gnomad_exomes_hom=0;gnomad_exomes_het=56;gnomad_genomes_an=251304;gnomad_genomes_hom=0;gnomad_genomes_het=369;clinvar_clinsig=benign;clinvar_rcv=RCV001353617;ANN=A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/23|c.591C>T|p.C197=|704/7088|591/5592|197/1864|44|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/22|c.450C>T|p.C150=|644/7028|450/5451|150/1817|44|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/22|c.591C>T|p.C197=|698/3696|591/2100|197/700|44|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/24|c.591C>T|p.C197=|704/7151|591/5655|197/1885|44| GT:AD:DP:GQ 0/0:52:52:99 0/0:46:46:99 0/1:21:42:99 -17 41252332 . T C . . ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-435A>G|p.?|555/7088|442/5592||-434|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-435A>G|p.?|495/7028|301/5451||-434|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-435A>G|p.?|549/3696|442/2100||-434|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-435A>G|p.?|555/7151|442/5655||-434| GT:AD:DP:GQ 0/0:25:25:75 0/1:14:28:99 0/1:19:40:99 -17 41252691 . ATATAAT A . . gnomad_exomes_an=2368;gnomad_exomes_hom=10;gnomad_exomes_het=80;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-800_442-795delATTATA|p.?|555/7088|442/5592||-794|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-795delATTATA|p.?|495/7028|301/5451||-794|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-795delATTATA|p.?|549/3696|442/2100||-794|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-795delATTATA|p.?|555/7151|442/5655||-794| GT:AD:DP:GQ 0/0:9:9:27 0/1:4:14:99 0/1:12:23:99 -17 41252693 . ATAAT A . . gnomad_exomes_an=3866;gnomad_exomes_hom=244;gnomad_exomes_het=618;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-800_442-797delATTA|p.?|555/7088|442/5592||-796|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-797delATTA|p.?|495/7028|301/5451||-796|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-797delATTA|p.?|549/3696|442/2100||-796|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-797delATTA|p.?|555/7151|442/5655||-796| GT:AD:DP:GQ 0/0:9:9:27 0/0:14:14:42 0/1:11:22:99 -17 41252695 . AAT A . . gnomad_exomes_an=5066;gnomad_exomes_hom=546;gnomad_exomes_het=795;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-800_442-799delAT|p.?|555/7088|442/5592||-798|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-799delAT|p.?|495/7028|301/5451||-798|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-799delAT|p.?|549/3696|442/2100||-798|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-799delAT|p.?|555/7151|442/5655||-798| GT:AD:DP:GQ 0/1:3:9:79 0/0:14:14:42 0/0:22:22:66 -17 41252696 . A T . . gnomad_exomes_an=4200;gnomad_exomes_hom=29;gnomad_exomes_het=334;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-799T>A|p.?|555/7088|442/5592||-798|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-799T>A|p.?|495/7028|301/5451||-798|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-799T>A|p.?|549/3696|442/2100||-798|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-799T>A|p.?|555/7151|442/5655||-798| GT:AD:DP:GQ 0/1:6:9:78 0/1:10:14:98 0/0:22:22:67 -17 41252697 . A AT . . ANN=AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-801_442-800insA|p.?|555/7088|442/5592||-800|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insA|p.?|495/7028|301/5451||-800|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insA|p.?|549/3696|442/2100||-800|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insA|p.?|555/7151|442/5655||-800| GT:AD:DP:GQ 1/1:0:45:99 1/2:0:33:99 1/2:1:33:99 -17 41252697 . A ATT . . ANN=ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-801_442-800insAA|p.?|555/7088|442/5592||-800|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insAA|p.?|495/7028|301/5451||-800|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insAA|p.?|549/3696|442/2100||-800|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insAA|p.?|555/7151|442/5655||-800| GT:AD:DP:GQ 1/1:45:45:99 1/2:17:33:99 1/2:11:33:99 -17 41254393 . G T . . gnomad_exomes_an=1936;gnomad_exomes_hom=0;gnomad_exomes_het=167;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1746C>A|p.?|554/7088|441/5592||1745|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1746C>A|p.?|494/7028|300/5451||1745|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1746C>A|p.?|548/3696|441/2100||1745|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1746C>A|p.?|554/7151|441/5655||1745| GT:AD:DP:GQ 0/1:29:37:66 ./.:.:.:. 0/0:32:35:47 -17 41273700 . C CA . . ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2333_80+2334insT|p.?|193/7088|80/5592||2333|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2333_-8+2334insT|p.?|187/7028|-8/5451||2333|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2333_80+2334insT|p.?|187/3696|80/2100||2333|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2333_80+2334insT|p.?|193/7151|80/5655||2333| GT:AD:DP:GQ 0/0:14:14:42 0/0:6:7:10 0/1:5:10:65 -MT 73 . A G . . . GT:AD:DP:GQ 0/0:3975:3975:99 1/1:0:2871:99 1/1:0:3320:99 -MT 119 . T C . . . GT:AD:DP:GQ 0/0:5417:5418:99 1/1:0:4039:99 1/1:1:4113:99 -MT 189 . A G . . . GT:AD:DP:GQ 0/0:3069:3069:99 1/1:0:1721:99 1/1:0:2204:99 -MT 195 . T C . . . GT:AD:DP:GQ 0/0:2599:2599:99 1/1:0:1592:99 1/1:0:1815:99 -MT 204 . T C . . . GT:AD:DP:GQ 0/0:2180:2180:99 1/1:0:1424:99 1/1:0:1304:99 -MT 207 . G A . . . GT:AD:DP:GQ 0/0:2115:2115:99 1/1:0:1408:99 1/1:0:1277:99 -MT 263 . A G . . . GT:AD:DP:GQ 1/1:0:1288:99 1/1:0:1204:99 1/1:0:1031:99 -MT 302 . A ACC . . . GT:AD:DP:GQ 0/1:157:844:99 0/0:1005:1011:99 0/0:800:803:99 -MT 310 . T TC . . . GT:AD:DP:GQ 1/1:0:1035:99 1/1:0:1411:99 1/1:1:1091:99 -MT 477 . T C . . . GT:AD:DP:GQ 1/1:4:2133:99 0/0:2266:2267:99 0/0:1725:1725:99 -MT 709 . G A . . . GT:AD:DP:GQ 0/0:2494:2494:99 1/1:0:2186:99 1/1:1:1814:99 -MT 750 . A G . . . GT:AD:DP:GQ 1/1:0:2757:99 1/1:0:2392:99 1/1:0:1621:99 -MT 879 . T C . . . GT:AD:DP:GQ 0/0:2853:2853:99 0/0:2784:2784:99 0/1:1351:1898:99 -MT 1243 . T C . . . GT:AD:DP:GQ 0/0:2674:2675:99 1/1:0:2198:99 1/1:0:1655:99 -MT 1438 . A G . . . GT:AD:DP:GQ 1/1:0:3815:99 1/1:0:3653:99 1/1:0:2900:99 -MT 1824 . T C . . . GT:AD:DP:GQ 1/1:0:2668:99 0/0:2409:2409:99 0/0:1752:1752:99 -MT 2633 . A G . . . GT:AD:DP:GQ 0/0:2535:2535:99 0/1:1648:2409:99 0/0:2269:2269:99 -MT 2706 . A G . . . GT:AD:DP:GQ 0/0:3200:3200:99 1/1:0:2847:99 1/1:0:2020:99 -MT 3010 . G A . . . GT:AD:DP:GQ 1/1:0:2841:99 0/0:2385:2385:99 0/0:1685:1685:99 -MT 3505 . A G . . . GT:AD:DP:GQ 0/0:2580:2594:99 1/1:0:2363:99 1/1:0:1664:99 -MT 3784 . T C . . . GT:AD:DP:GQ 0/1:480:2936:99 0/0:2504:2504:99 0/0:1991:1991:99 -MT 4769 . A G . . . GT:AD:DP:GQ 1/1:0:2689:99 1/1:0:2549:99 1/1:0:2108:99 -MT 5046 . G A . . . GT:AD:DP:GQ 0/0:2876:2878:99 1/1:0:2466:99 1/1:0:1661:99 -MT 5460 . G A . . . GT:AD:DP:GQ 0/0:2905:2907:99 1/1:0:2759:99 1/1:2:1970:99 -MT 7028 . C T . . . GT:AD:DP:GQ 0/0:2577:2580:99 1/1:2:2203:99 1/1:1:1946:99 -MT 7864 . C T . . . GT:AD:DP:GQ 0/0:3588:3589:99 1/1:0:3465:99 1/1:0:2746:99 -MT 8170 . A G . . . GT:AD:DP:GQ 0/0:2051:2052:99 1/1:0:2257:99 1/1:0:1774:99 -MT 8251 . G A . . . GT:AD:DP:GQ 0/0:2360:2360:99 1/1:0:2317:99 1/1:1:1625:99 -MT 8860 . A G . . . GT:AD:DP:GQ 1/1:0:3278:99 1/1:0:3088:99 1/1:0:2241:99 -MT 8994 . G A . . . GT:AD:DP:GQ 0/0:2793:2793:99 1/1:0:2368:99 1/1:1:1918:99 -MT 9007 . A G . . . GT:AD:DP:GQ 1/1:0:2959:99 0/0:2442:2442:99 0/0:1735:1735:99 -MT 9150 . A G . . . GT:AD:DP:GQ 1/1:0:3163:99 0/0:3538:3538:99 0/0:2767:2767:99 -MT 9380 . G A . . . GT:AD:DP:GQ 1/1:1:3321:99 0/0:3222:3222:99 0/0:2547:2547:99 -MT 10097 . A G . . . GT:AD:DP:GQ 0/0:2660:2660:99 0/1:1680:2188:99 0/0:1851:1851:99 -MT 11204 . T C . . . GT:AD:DP:GQ 0/0:3168:3173:99 1/1:0:2922:99 1/1:0:2418:99 -MT 11674 . C T . . . GT:AD:DP:GQ 0/0:2890:2890:99 1/1:0:2666:99 1/1:1:2180:99 -MT 11719 . G A . . . GT:AD:DP:GQ 0/0:3339:3341:99 1/1:0:3052:99 1/1:0:2203:99 -MT 11947 . A G . . . GT:AD:DP:GQ 0/0:2579:2581:99 1/1:0:2273:99 1/1:0:1804:99 -MT 12414 . T C . . . GT:AD:DP:GQ 0/0:2852:2855:99 1/1:1:2546:99 1/1:0:1733:99 -MT 12648 . A G . . . GT:AD:DP:GQ 0/0:1812:1813:99 1/1:2:1664:99 1/1:4:1781:99 -MT 12705 . C T . . . GT:AD:DP:GQ 0/0:2359:2369:99 1/1:1:2138:99 1/1:1:1622:99 -MT 13406 . G A . . . GT:AD:DP:GQ 0/0:2539:2540:99 0/0:2216:2216:99 0/1:1224:1957:99 -MT 13611 . A G . . . GT:AD:DP:GQ 0/0:3838:3840:99 1/1:0:3717:99 1/1:1:2835:99 -MT 13928 . G C . . . GT:AD:DP:GQ 0/0:2947:2947:99 1/1:0:2700:99 1/1:0:1880:99 -MT 14148 . A G . . . GT:AD:DP:GQ 0/0:3019:3021:99 1/1:0:2820:99 1/1:0:1962:99 -MT 14766 . C T . . . GT:AD:DP:GQ 0/0:3318:3321:99 1/1:2:3113:99 1/1:3:2358:99 -MT 15326 . A G . . . GT:AD:DP:GQ 1/1:0:3716:99 1/1:0:3560:99 1/1:0:2690:99 -MT 15884 . G C . . . GT:AD:DP:GQ 0/0:3595:3596:99 1/1:0:3167:99 1/1:1:2734:99 -MT 16184 . C T . . . GT:AD:DP:GQ 0/0:1406:1407:99 1/1:0:1969:99 1/1:0:1478:99 -MT 16223 . C T . . . GT:AD:DP:GQ 0/0:1405:1406:99 1/1:0:2018:99 1/1:0:1472:99 -MT 16263 . T C . . . GT:AD:DP:GQ 1/1:2:1478:99 0/0:1994:1994:99 0/0:1475:1475:99 -MT 16292 . C T . . . GT:AD:DP:GQ 0/0:1652:1652:99 1/1:1:1914:99 1/1:0:1476:99 -MT 16519 . T C . . . GT:AD:DP:GQ 1/1:0:1759:99 1/1:0:4094:99 1/1:0:1744:99 +17 41249263 . G A . . gnomad_exomes_an=31398;gnomad_exomes_hom=0;gnomad_exomes_het=56;gnomad_genomes_an=251304;gnomad_genomes_hom=0;gnomad_genomes_het=369;clinvar_clinsig=benign;clinvar_rcv=RCV000112746;clinvar_vcv=VCV000055642;ANN=A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/23|c.591C>T|p.C197=|704/7088|591/5592|197/1864|44|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/22|c.450C>T|p.C150=|644/7028|450/5451|150/1817|44|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/22|c.591C>T|p.C197=|698/3696|591/2100|197/700|44|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/24|c.591C>T|p.C197=|704/7151|591/5655|197/1885|44| GT:AD:DP:GQ 0/0:52,0:52:99 0/0:46,0:46:99 0/1:21,21:42:99 +17 41252332 . T C . . ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-435A>G|p.?|555/7088|442/5592||-434|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-435A>G|p.?|495/7028|301/5451||-434|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-435A>G|p.?|549/3696|442/2100||-434|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-435A>G|p.?|555/7151|442/5655||-434| GT:AD:DP:GQ 0/0:25,0:25:75 0/1:14,14:28:99 0/1:19,21:40:99 +17 41252691 . ATATAAT A . . gnomad_exomes_an=2368;gnomad_exomes_hom=10;gnomad_exomes_het=80;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-800_442-795delATTATA|p.?|555/7088|442/5592||-794|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-795delATTATA|p.?|495/7028|301/5451||-794|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-795delATTATA|p.?|549/3696|442/2100||-794|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-795delATTATA|p.?|555/7151|442/5655||-794| GT:AD:DP:GQ 0/0:9,0:9:27 0/1:4,10:14:99 0/1:12,11:23:99 +17 41252693 . ATAAT A . . gnomad_exomes_an=3866;gnomad_exomes_hom=244;gnomad_exomes_het=618;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-800_442-797delATTA|p.?|555/7088|442/5592||-796|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-797delATTA|p.?|495/7028|301/5451||-796|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-797delATTA|p.?|549/3696|442/2100||-796|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-797delATTA|p.?|555/7151|442/5655||-796| GT:AD:DP:GQ 0/0:9,0:9:27 0/0:14,0:14:42 0/1:11,11:22:99 +17 41252695 . AAT A . . gnomad_exomes_an=5066;gnomad_exomes_hom=546;gnomad_exomes_het=795;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-800_442-799delAT|p.?|555/7088|442/5592||-798|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-799delAT|p.?|495/7028|301/5451||-798|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-799delAT|p.?|549/3696|442/2100||-798|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-799delAT|p.?|555/7151|442/5655||-798| GT:AD:DP:GQ 0/1:3,6:9:79 0/0:14,0:14:42 0/0:22,0:22:66 +17 41252696 . A T . . gnomad_exomes_an=4200;gnomad_exomes_hom=29;gnomad_exomes_het=334;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-799T>A|p.?|555/7088|442/5592||-798|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-799T>A|p.?|495/7028|301/5451||-798|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-799T>A|p.?|549/3696|442/2100||-798|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-799T>A|p.?|555/7151|442/5655||-798| GT:AD:DP:GQ 0/1:6,3:9:78 0/1:10,4:14:98 0/0:22,0:22:67 +17 41252697 . A AT . . ANN=AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-801_442-800insA|p.?|555/7088|442/5592||-800|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insA|p.?|495/7028|301/5451||-800|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insA|p.?|549/3696|442/2100||-800|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insA|p.?|555/7151|442/5655||-800| GT:AD:DP:GQ 1/1:0,45:45:99 1/0:16,17:33:99 1/0:22,11:33:99 +17 41252697 . A ATT . . ANN=ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-801_442-800insAA|p.?|555/7088|442/5592||-800|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insAA|p.?|495/7028|301/5451||-800|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insAA|p.?|549/3696|442/2100||-800|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insAA|p.?|555/7151|442/5655||-800| GT:AD:DP:GQ 0/0:45,0:45:99 0/1:17,16:33:99 0/1:12,21:33:99 +17 41254393 . G T . . gnomad_exomes_an=1936;gnomad_exomes_hom=0;gnomad_exomes_het=167;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1746C>A|p.?|554/7088|441/5592||1745|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1746C>A|p.?|494/7028|300/5451||1745|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1746C>A|p.?|548/3696|441/2100||1745|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1746C>A|p.?|554/7151|441/5655||1745| GT:AD:DP:GQ 0/1:29,8:37:66 ./.:.:.:. 0/0:32,3:35:47 +17 41273700 . C CA . . ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2333_80+2334insT|p.?|193/7088|80/5592||2333|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2333_-8+2334insT|p.?|187/7028|-8/5451||2333|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2333_80+2334insT|p.?|187/3696|80/2100||2333|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2333_80+2334insT|p.?|193/7151|80/5655||2333| GT:AD:DP:GQ 0/0:14,0:14:42 0/0:6,1:7:10 0/1:5,5:10:65 +MT 73 . A G . . . GT:AD:DP:GQ 0/0:3975,0:3975:99 1/1:0,2871:2871:99 1/1:0,3320:3320:99 +MT 119 . T C . . . GT:AD:DP:GQ 0/0:5417,1:5418:99 1/1:0,4039:4039:99 1/1:1,4112:4113:99 +MT 189 . A G . . . GT:AD:DP:GQ 0/0:3069,0:3069:99 1/1:0,1721:1721:99 1/1:0,2204:2204:99 +MT 195 . T C . . . GT:AD:DP:GQ 0/0:2599,0:2599:99 1/1:0,1592:1592:99 1/1:0,1815:1815:99 +MT 204 . T C . . . GT:AD:DP:GQ 0/0:2180,0:2180:99 1/1:0,1424:1424:99 1/1:0,1304:1304:99 +MT 207 . G A . . . GT:AD:DP:GQ 0/0:2115,0:2115:99 1/1:0,1408:1408:99 1/1:0,1277:1277:99 +MT 263 . A G . . . GT:AD:DP:GQ 1/1:0,1288:1288:99 1/1:0,1204:1204:99 1/1:0,1031:1031:99 +MT 302 . A ACC . . . GT:AD:DP:GQ 0/1:157,687:844:99 0/0:1005,6:1011:99 0/0:800,3:803:99 +MT 310 . T TC . . . GT:AD:DP:GQ 1/1:0,1035:1035:99 1/1:0,1411:1411:99 1/1:1,1090:1091:99 +MT 477 . T C . . . GT:AD:DP:GQ 1/1:4,2129:2133:99 0/0:2266,1:2267:99 0/0:1725,0:1725:99 +MT 709 . G A . . . GT:AD:DP:GQ 0/0:2494,0:2494:99 1/1:0,2186:2186:99 1/1:1,1813:1814:99 +MT 750 . A G . . . GT:AD:DP:GQ 1/1:0,2757:2757:99 1/1:0,2392:2392:99 1/1:0,1621:1621:99 +MT 879 . T C . . . GT:AD:DP:GQ 0/0:2853,0:2853:99 0/0:2784,0:2784:99 0/1:1351,547:1898:99 +MT 1243 . T C . . . GT:AD:DP:GQ 0/0:2674,1:2675:99 1/1:0,2198:2198:99 1/1:0,1655:1655:99 +MT 1438 . A G . . . GT:AD:DP:GQ 1/1:0,3815:3815:99 1/1:0,3653:3653:99 1/1:0,2900:2900:99 +MT 1824 . T C . . . GT:AD:DP:GQ 1/1:0,2668:2668:99 0/0:2409,0:2409:99 0/0:1752,0:1752:99 +MT 2633 . A G . . . GT:AD:DP:GQ 0/0:2535,0:2535:99 0/1:1648,761:2409:99 0/0:2269,0:2269:99 +MT 2706 . A G . . . GT:AD:DP:GQ 0/0:3200,0:3200:99 1/1:0,2847:2847:99 1/1:0,2020:2020:99 +MT 3010 . G A . . . GT:AD:DP:GQ 1/1:0,2841:2841:99 0/0:2385,0:2385:99 0/0:1685,0:1685:99 +MT 3505 . A G . . . GT:AD:DP:GQ 0/0:2580,14:2594:99 1/1:0,2363:2363:99 1/1:0,1664:1664:99 +MT 3784 . T C . . . GT:AD:DP:GQ 0/1:480,2456:2936:99 0/0:2504,0:2504:99 0/0:1991,0:1991:99 +MT 4769 . A G . . . GT:AD:DP:GQ 1/1:0,2689:2689:99 1/1:0,2549:2549:99 1/1:0,2108:2108:99 +MT 5046 . G A . . . GT:AD:DP:GQ 0/0:2876,2:2878:99 1/1:0,2466:2466:99 1/1:0,1661:1661:99 +MT 5460 . G A . . . GT:AD:DP:GQ 0/0:2905,2:2907:99 1/1:0,2759:2759:99 1/1:2,1968:1970:99 +MT 7028 . C T . . . GT:AD:DP:GQ 0/0:2577,3:2580:99 1/1:2,2201:2203:99 1/1:1,1945:1946:99 +MT 7864 . C T . . . GT:AD:DP:GQ 0/0:3588,1:3589:99 1/1:0,3465:3465:99 1/1:0,2746:2746:99 +MT 8170 . A G . . . GT:AD:DP:GQ 0/0:2051,1:2052:99 1/1:0,2257:2257:99 1/1:0,1774:1774:99 +MT 8251 . G A . . . GT:AD:DP:GQ 0/0:2360,0:2360:99 1/1:0,2317:2317:99 1/1:1,1624:1625:99 +MT 8860 . A G . . . GT:AD:DP:GQ 1/1:0,3278:3278:99 1/1:0,3088:3088:99 1/1:0,2241:2241:99 +MT 8994 . G A . . . GT:AD:DP:GQ 0/0:2793,0:2793:99 1/1:0,2368:2368:99 1/1:1,1917:1918:99 +MT 9007 . A G . . . GT:AD:DP:GQ 1/1:0,2959:2959:99 0/0:2442,0:2442:99 0/0:1735,0:1735:99 +MT 9150 . A G . . . GT:AD:DP:GQ 1/1:0,3163:3163:99 0/0:3538,0:3538:99 0/0:2767,0:2767:99 +MT 9380 . G A . . . GT:AD:DP:GQ 1/1:1,3320:3321:99 0/0:3222,0:3222:99 0/0:2547,0:2547:99 +MT 10097 . A G . . . GT:AD:DP:GQ 0/0:2660,0:2660:99 0/1:1680,508:2188:99 0/0:1851,0:1851:99 +MT 11204 . T C . . . GT:AD:DP:GQ 0/0:3168,5:3173:99 1/1:0,2922:2922:99 1/1:0,2418:2418:99 +MT 11674 . C T . . . GT:AD:DP:GQ 0/0:2890,0:2890:99 1/1:0,2666:2666:99 1/1:1,2179:2180:99 +MT 11719 . G A . . . GT:AD:DP:GQ 0/0:3339,2:3341:99 1/1:0,3052:3052:99 1/1:0,2203:2203:99 +MT 11947 . A G . . . GT:AD:DP:GQ 0/0:2579,2:2581:99 1/1:0,2273:2273:99 1/1:0,1804:1804:99 +MT 12414 . T C . . . GT:AD:DP:GQ 0/0:2852,3:2855:99 1/1:1,2545:2546:99 1/1:0,1733:1733:99 +MT 12648 . A G . . . GT:AD:DP:GQ 0/0:1812,1:1813:99 1/1:2,1662:1664:99 1/1:4,1777:1781:99 +MT 12705 . C T . . . GT:AD:DP:GQ 0/0:2359,10:2369:99 1/1:1,2137:2138:99 1/1:1,1621:1622:99 +MT 13406 . G A . . . GT:AD:DP:GQ 0/0:2539,1:2540:99 0/0:2216,0:2216:99 0/1:1224,733:1957:99 +MT 13611 . A G . . . GT:AD:DP:GQ 0/0:3838,2:3840:99 1/1:0,3717:3717:99 1/1:1,2834:2835:99 +MT 13928 . G C . . . GT:AD:DP:GQ 0/0:2947,0:2947:99 1/1:0,2700:2700:99 1/1:0,1880:1880:99 +MT 14148 . A G . . . GT:AD:DP:GQ 0/0:3019,2:3021:99 1/1:0,2820:2820:99 1/1:0,1962:1962:99 +MT 14766 . C T . . . GT:AD:DP:GQ 0/0:3318,3:3321:99 1/1:2,3111:3113:99 1/1:3,2355:2358:99 +MT 15326 . A G . . . GT:AD:DP:GQ 1/1:0,3716:3716:99 1/1:0,3560:3560:99 1/1:0,2690:2690:99 +MT 15884 . G C . . . GT:AD:DP:GQ 0/0:3595,1:3596:99 1/1:0,3167:3167:99 1/1:1,2733:2734:99 +MT 16184 . C T . . . GT:AD:DP:GQ 0/0:1406,1:1407:99 1/1:0,1969:1969:99 1/1:0,1478:1478:99 +MT 16223 . C T . . . GT:AD:DP:GQ 0/0:1405,1:1406:99 1/1:0,2018:2018:99 1/1:0,1472:1472:99 +MT 16263 . T C . . . GT:AD:DP:GQ 1/1:2,1476:1478:99 0/0:1994,0:1994:99 0/0:1475,0:1475:99 +MT 16292 . C T . . . GT:AD:DP:GQ 0/0:1652,0:1652:99 1/1:1,1913:1914:99 1/1:0,1476:1476:99 +MT 16519 . T C . . . GT:AD:DP:GQ 1/1:0,1759:1759:99 1/1:0,4094:4094:99 1/1:0,1744:1744:99 diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@NA12878_dragen_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@NA12878_dragen_vcf.snap index a1716f1a..f339a619 100644 --- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@NA12878_dragen_vcf.snap +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@NA12878_dragen_vcf.snap @@ -53,133 +53,133 @@ expression: "std::fs::read_to_string(&args.path_out)?" ##x-varfish-version= ##x-varfish-version= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 -17 41244000 . T C . . gnomad_exomes_an=31346;gnomad_exomes_hom=1591;gnomad_exomes_het=6707;gnomad_genomes_an=250954;gnomad_genomes_hom=16402;gnomad_genomes_het=55703;clinvar_clinsig=benign;clinvar_rcv=RCV002490466;ANN=C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|10/23|c.3548A>G|p.K1183R|3661/7088|3548/5592|1183/1864|2878|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.3407A>G|p.K1136R|3601/7028|3407/5451|1136/1817|2878|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.788-951A>G|p.?|895/3696|788/2100||-950|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.3548A>G|p.K1183R|3661/7151|3548/5655|1183/1885|2878| GT:AD:DP:GQ 0/1:8:26:43 -17 41244435 . T C . . gnomad_exomes_an=31332;gnomad_exomes_hom=1505;gnomad_exomes_het=6415;gnomad_genomes_an=251032;gnomad_genomes_hom=16145;gnomad_genomes_het=55137;clinvar_clinsig=benign;clinvar_rcv=RCV001269365;ANN=C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|10/23|c.3113A>G|p.E1038G|3226/7088|3113/5592|1038/1864|2443|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2972A>G|p.E991G|3166/7028|2972/5451|991/1817|2443|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.788-1386A>G|p.?|895/3696|788/2100||-1385|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.3113A>G|p.E1038G|3226/7151|3113/5655|1038/1885|2443| GT:AD:DP:GQ 0/1:12:26:47 -17 41244936 . G A . . gnomad_exomes_an=31324;gnomad_exomes_hom=4287;gnomad_exomes_het=6594;gnomad_genomes_an=251034;gnomad_genomes_hom=22738;gnomad_genomes_het=55898;clinvar_clinsig=benign;clinvar_rcv=RCV002496522;ANN=A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|10/23|c.2612C>T|p.P871L|2725/7088|2612/5592|871/1864|1942|,A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2471C>T|p.P824L|2665/7028|2471/5451|824/1817|1942|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1825C>T|p.?|894/3696|787/2100||1824|,A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2612C>T|p.P871L|2725/7151|2612/5655|871/1885|1942| GT:AD:DP:GQ 0/1:17:30:47 -17 41245237 . A G . . gnomad_exomes_an=31314;gnomad_exomes_hom=1492;gnomad_exomes_het=6416;gnomad_genomes_an=250946;gnomad_genomes_hom=16057;gnomad_genomes_het=55063;clinvar_clinsig=benign;clinvar_rcv=RCV000755639;ANN=G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|10/23|c.2311T>C|p.L771=|2424/7088|2311/5592|771/1864|-1786|,G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2170T>C|p.L724=|2364/7028|2170/5451|724/1817|-1786|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1524T>C|p.?|894/3696|787/2100||1523|,G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2311T>C|p.L771=|2424/7151|2311/5655|771/1885|-1786| GT:AD:DP:GQ 0/1:18:29:46 -17 41245466 . G A . . gnomad_exomes_an=31338;gnomad_exomes_hom=1602;gnomad_exomes_het=6709;gnomad_genomes_an=251110;gnomad_genomes_hom=16420;gnomad_genomes_het=55707;clinvar_clinsig=benign;clinvar_rcv=RCV002477262;ANN=A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|10/23|c.2082C>T|p.S694=|2195/7088|2082/5592|694/1864|-2015|,A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.1941C>T|p.S647=|2135/7028|1941/5451|647/1817|-2015|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1295C>T|p.?|894/3696|787/2100||1294|,A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2082C>T|p.S694=|2195/7151|2082/5655|694/1885|-2015| GT:AD:DP:GQ 0/1:11:19:48 -17 41247122 . A ACCT . . gnomad_exomes_an=31242;gnomad_exomes_hom=1750;gnomad_exomes_het=7017;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001709486;ANN=ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|9/22|c.671-246_671-245insAGG|p.?|784/7088|671/5592||-245|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|8/21|c.530-246_530-245insAGG|p.?|724/7028|530/5451||-245|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|9/21|c.671-246_671-245insAGG|p.?|778/3696|671/2100||-245|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|9/23|c.671-246_671-245insAGG|p.?|784/7151|671/5655||-245| GT:AD:DP:GQ 0/1:18:29:45 -17 41247604 . A C . . gnomad_exomes_an=30832;gnomad_exomes_hom=1544;gnomad_exomes_het=6574;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001636715;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|9/22|c.670+259T>G|p.?|783/7088|670/5592||258|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|8/21|c.529+259T>G|p.?|723/7028|529/5451||258|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|9/21|c.670+259T>G|p.?|777/3696|670/2100||258|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|9/23|c.670+259T>G|p.?|783/7151|670/5655||258| GT:AD:DP:GQ 0/1:12:23:47 -17 41248164 . C T . . gnomad_exomes_an=31116;gnomad_exomes_hom=1468;gnomad_exomes_het=6372;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001668352;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/22|c.594-225G>A|p.?|707/7088|594/5592||-224|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-225G>A|p.?|647/7028|453/5451||-224|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-225G>A|p.?|701/3696|594/2100||-224|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-225G>A|p.?|707/7151|594/5655||-224| GT:AD:DP:GQ 0/1:14:21:44 -17 41248393 . C CAAAAAAAAAA . . ANN=CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/22|c.594-455_594-454insTTTTTTTTTT|p.?|707/7088|594/5592||-454|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-455_453-454insTTTTTTTTTT|p.?|647/7028|453/5451||-454|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-455_594-454insTTTTTTTTTT|p.?|701/3696|594/2100||-454|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-455_594-454insTTTTTTTTTT|p.?|707/7151|594/5655||-454| GT:AD:DP:GQ 0/1:9:16:48 -17 41248484 . G C . . gnomad_exomes_an=30426;gnomad_exomes_hom=1385;gnomad_exomes_het=6148;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001657973;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/22|c.594-545C>G|p.?|707/7088|594/5592||-544|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-545C>G|p.?|647/7028|453/5451||-544|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-545C>G|p.?|701/3696|594/2100||-544|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-545C>G|p.?|707/7151|594/5655||-544| GT:AD:DP:GQ 0/1:11:20:48 -17 41248588 . CA C . . gnomad_exomes_an=12806;gnomad_exomes_hom=585;gnomad_exomes_het=4704;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/22|c.594-650delT|p.?|707/7088|594/5592||-649|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-650delT|p.?|647/7028|453/5451||-649|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-650delT|p.?|701/3696|594/2100||-649|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-650delT|p.?|707/7151|594/5655||-649| GT:AD:DP:GQ 0/1:9:19:42 -17 41249094 . A G . . gnomad_exomes_an=31332;gnomad_exomes_hom=1602;gnomad_exomes_het=6703;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001610505;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/22|c.593+167T>C|p.?|706/7088|593/5592||166|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.452+167T>C|p.?|646/7028|452/5451||166|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.593+167T>C|p.?|700/3696|593/2100||166|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.593+167T>C|p.?|706/7151|593/5655||166| GT:AD:DP:GQ 0/1:9:16:48 -17 41249363 . TA T . . gnomad_exomes_an=31286;gnomad_exomes_hom=1497;gnomad_exomes_het=6409;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.548-58delT|p.?|661/7088|548/5592||-57|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.407-58delT|p.?|601/7028|407/5451||-57|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.548-58delT|p.?|655/3696|548/2100||-57|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.548-58delT|p.?|661/7151|548/5655||-57| GT:AD:DP:GQ 0/1:12:25:48 -17 41250047 . C CT . . gnomad_exomes_an=22188;gnomad_exomes_hom=992;gnomad_exomes_het=4281;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.548-742_548-741insA|p.?|661/7088|548/5592||-741|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.407-742_407-741insA|p.?|601/7028|407/5451||-741|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.548-742_548-741insA|p.?|655/3696|548/2100||-741|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.548-742_548-741insA|p.?|661/7151|548/5655||-741| GT:AD:DP:GQ 0/1:13:20:18 -17 41250678 . C CT . . gnomad_exomes_an=31058;gnomad_exomes_hom=1566;gnomad_exomes_het=6658;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191403;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.547+1113_547+1114insA|p.?|660/7088|547/5592||1113|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+1113_406+1114insA|p.?|600/7028|406/5451||1113|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+1113_547+1114insA|p.?|654/3696|547/2100||1113|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+1113_547+1114insA|p.?|660/7151|547/5655||1113| GT:AD:DP:GQ 0/1:6:22:42 -17 41250923 . T C . . gnomad_exomes_an=29782;gnomad_exomes_hom=4187;gnomad_exomes_het=6234;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191405;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.547+869A>G|p.?|660/7088|547/5592||868|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+869A>G|p.?|600/7028|406/5451||868|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+869A>G|p.?|654/3696|547/2100||868|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+869A>G|p.?|660/7151|547/5655||868| GT:AD:DP:GQ 0/1:13:22:47 -17 41251495 . C G . . gnomad_exomes_an=30850;gnomad_exomes_hom=1491;gnomad_exomes_het=6363;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001640278;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.547+297G>C|p.?|660/7088|547/5592||296|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+297G>C|p.?|600/7028|406/5451||296|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+297G>C|p.?|654/3696|547/2100||296|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+297G>C|p.?|660/7151|547/5655||296| GT:AD:DP:GQ 0/1:11:26:48 -17 41251646 . T A . . gnomad_exomes_an=31294;gnomad_exomes_hom=1592;gnomad_exomes_het=6693;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV002345409;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.547+146A>T|p.?|660/7088|547/5592||145|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+146A>T|p.?|600/7028|406/5451||145|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+146A>T|p.?|654/3696|547/2100||145|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+146A>T|p.?|660/7151|547/5655||145| GT:AD:DP:GQ 0/1:11:19:48 -17 41252575 . G A . . gnomad_exomes_an=6888;gnomad_exomes_hom=193;gnomad_exomes_het=1277;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191411;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-678C>T|p.?|555/7088|442/5592||-677|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-678C>T|p.?|495/7028|301/5451||-677|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-678C>T|p.?|549/3696|442/2100||-677|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-678C>T|p.?|555/7151|442/5655||-677| GT:AD:DP:GQ:PS 1|1:0:3:5:41252575 -17 41252591 . C CAT . . gnomad_exomes_an=10332;gnomad_exomes_hom=95;gnomad_exomes_het=571;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-695_442-694insAT|p.?|555/7088|442/5592||-694|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-695_301-694insAT|p.?|495/7028|301/5451||-694|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-695_442-694insAT|p.?|549/3696|442/2100||-694|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-695_442-694insAT|p.?|555/7151|442/5655||-694| GT:AD:DP:GQ:PS 1|1:0:2:4:41252575 -17 41254174 . A G . . gnomad_exomes_an=30142;gnomad_exomes_hom=1576;gnomad_exomes_het=6550;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191423;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1965T>C|p.?|554/7088|441/5592||1964|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1965T>C|p.?|494/7028|300/5451||1964|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1965T>C|p.?|548/3696|441/2100||1964|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1965T>C|p.?|554/7151|441/5655||1964| GT:AD:DP:GQ 0/1:14:27:48 -17 41254374 . C CTTTTTTTT . . gnomad_exomes_an=15994;gnomad_exomes_hom=494;gnomad_exomes_het=1743;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1764_441+1765insAAAAAAAA|p.?|554/7088|441/5592||1764|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1764_300+1765insAAAAAAAA|p.?|494/7028|300/5451||1764|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1764_441+1765insAAAAAAAA|p.?|548/3696|441/2100||1764|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1764_441+1765insAAAAAAAA|p.?|554/7151|441/5655||1764| GT:AD:DP:GQ 0/1:6:13:48 -17 41254405 . C T . . gnomad_exomes_an=24316;gnomad_exomes_hom=1000;gnomad_exomes_het=4795;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000256092;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1734G>A|p.?|554/7088|441/5592||1733|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1734G>A|p.?|494/7028|300/5451||1733|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1734G>A|p.?|548/3696|441/2100||1733|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1734G>A|p.?|554/7151|441/5655||1733| GT:AD:DP:GQ 0/1:5:14:43 -17 41254486 . T G . . gnomad_exomes_an=30560;gnomad_exomes_hom=4284;gnomad_exomes_het=6345;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191424;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1653A>C|p.?|554/7088|441/5592||1652|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1653A>C|p.?|494/7028|300/5451||1652|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1653A>C|p.?|548/3696|441/2100||1652|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1653A>C|p.?|554/7151|441/5655||1652| GT:AD:DP:GQ 0/1:8:23:46 -17 41254965 . C CT . . gnomad_exomes_an=26726;gnomad_exomes_hom=2359;gnomad_exomes_het=6380;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255713;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1173_441+1174insA|p.?|554/7088|441/5592||1173|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1173_300+1174insA|p.?|494/7028|300/5451||1173|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1173_441+1174insA|p.?|548/3696|441/2100||1173|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1173_441+1174insA|p.?|554/7151|441/5655||1173| GT:AD:DP:GQ 0/1:14:22:22 -17 41255102 . A G . . gnomad_exomes_an=31104;gnomad_exomes_hom=1426;gnomad_exomes_het=6400;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191428;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1037T>C|p.?|554/7088|441/5592||1036|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1037T>C|p.?|494/7028|300/5451||1036|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1037T>C|p.?|548/3696|441/2100||1036|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1037T>C|p.?|554/7151|441/5655||1036| GT:AD:DP:GQ:PS 0|1:19:31:46:41255102 -17 41255111 . A T . . gnomad_exomes_an=31114;gnomad_exomes_hom=1530;gnomad_exomes_het=6684;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191429;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1028T>A|p.?|554/7088|441/5592||1027|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1028T>A|p.?|494/7028|300/5451||1027|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1028T>A|p.?|548/3696|441/2100||1027|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1028T>A|p.?|554/7151|441/5655||1027| GT:AD:DP:GQ:PS 0|1:19:31:46:41255102 -17 41256074 . CA C . . gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+64delT|p.?|554/7088|441/5592||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||63| GT:AD:DP:GQ:PS 0|1:11:17:43:41256074 -17 41256089 . AAAAAAAAAGAAAAG A . . gnomad_exomes_an=28388;gnomad_exomes_hom=1079;gnomad_exomes_het=5744;gnomad_genomes_an=167932;gnomad_genomes_hom=9911;gnomad_genomes_het=23697;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|554/7088|441/5592||35|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+36_300+49delCTTTTCTTTTTTTT|p.?|494/7028|300/5451||35|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|548/3696|441/2100||35|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|554/7151|441/5655||35| GT:AD:DP:GQ:PS 0|1:13:19:43:41256074 -17 41257134 . T C . . gnomad_exomes_an=31346;gnomad_exomes_hom=4418;gnomad_exomes_het=6505;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV002415590;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|4/22|c.213-161A>G|p.?|326/7088|213/5592||-160|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.72-161A>G|p.?|266/7028|72/5451||-160|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.213-161A>G|p.?|320/3696|213/2100||-160|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.213-161A>G|p.?|326/7151|213/5655||-160| GT:AD:DP:GQ 0/1:14:29:48 -17 41257458 . A C . . gnomad_exomes_an=31258;gnomad_exomes_hom=1500;gnomad_exomes_het=6414;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191434;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|4/22|c.213-485T>G|p.?|326/7088|213/5592||-484|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.72-485T>G|p.?|266/7028|72/5451||-484|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.213-485T>G|p.?|320/3696|213/2100||-484|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.213-485T>G|p.?|326/7151|213/5655||-484| GT:AD:DP:GQ 0/1:11:26:48 -17 41258043 . C T . . gnomad_exomes_an=30426;gnomad_exomes_hom=1538;gnomad_exomes_het=6460;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191436;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|4/22|c.212+430G>A|p.?|325/7088|212/5592||429|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.71+430G>A|p.?|265/7028|71/5451||429|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.212+430G>A|p.?|319/3696|212/2100||429|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.212+430G>A|p.?|325/7151|212/5655||429| GT:AD:DP:GQ 0/1:14:27:48 -17 41258135 . T TA . . gnomad_exomes_an=20132;gnomad_exomes_hom=1;gnomad_exomes_het=267;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|4/22|c.212+337_212+338insT|p.?|325/7088|212/5592||337|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.71+337_71+338insT|p.?|265/7028|71/5451||337|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.212+337_212+338insT|p.?|319/3696|212/2100||337|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.212+337_212+338insT|p.?|325/7151|212/5655||337| GT:AD:DP:GQ 1/1:3:14:4 -17 41259049 . C T . . gnomad_exomes_an=30790;gnomad_exomes_hom=1585;gnomad_exomes_het=6633;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191440;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-499G>A|p.?|248/7088|135/5592||-498|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-499G>A|p.?|188/7028|-7/5451||-498|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-499G>A|p.?|242/3696|135/2100||-498|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-499G>A|p.?|248/7151|135/5655||-498| GT:AD:DP:GQ 0/1:8:16:48 -17 41259079 . A ATT . . gnomad_exomes_an=21472;gnomad_exomes_hom=898;gnomad_exomes_het=3635;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-530_135-529insAA|p.?|248/7088|135/5592||-529|,ATT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-530_-7-529insAA|p.?|188/7028|-7/5451||-529|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-530_135-529insAA|p.?|242/3696|135/2100||-529|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-530_135-529insAA|p.?|248/7151|135/5655||-529| GT:AD:DP:GQ 0/1:10:13:7 -17 41259113 . G A . . gnomad_exomes_an=26218;gnomad_exomes_hom=2;gnomad_exomes_het=204;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255936;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-563C>T|p.?|248/7088|135/5592||-562|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-563C>T|p.?|188/7028|-7/5451||-562|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-563C>T|p.?|242/3696|135/2100||-562|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-563C>T|p.?|248/7151|135/5655||-562| GT:AD:DP:GQ 0/1:11:19:48 -17 41260352 . C CA . . gnomad_exomes_an=19754;gnomad_exomes_hom=856;gnomad_exomes_het=4728;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255985;ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-1803_135-1802insT|p.?|248/7088|135/5592||-1802|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-1803_-7-1802insT|p.?|188/7028|-7/5451||-1802|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-1803_135-1802insT|p.?|242/3696|135/2100||-1802|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-1803_135-1802insT|p.?|248/7151|135/5655||-1802| GT:AD:DP:GQ 0/1:11:19:43 -17 41260723 . C CAAAAA . . ANN=CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-2174_135-2173insTTTTT|p.?|248/7088|135/5592||-2173|,CAAAAA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2174_-7-2173insTTTTT|p.?|188/7028|-7/5451||-2173|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2174_135-2173insTTTTT|p.?|242/3696|135/2100||-2173|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2174_135-2173insTTTTT|p.?|248/7151|135/5655||-2173| GT:AD:DP:GQ 0/1:1:2:20 -17 41260808 . A G . . gnomad_exomes_an=30782;gnomad_exomes_hom=1558;gnomad_exomes_het=6565;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191445;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-2258T>C|p.?|248/7088|135/5592||-2257|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2258T>C|p.?|188/7028|-7/5451||-2257|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2258T>C|p.?|242/3696|135/2100||-2257|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2258T>C|p.?|248/7151|135/5655||-2257| GT:AD:DP:GQ 0/1:12:15:32 -17 41261058 . T TCTATCTATCTACCTAC . . gnomad_exomes_an=31232;gnomad_exomes_hom=1461;gnomad_exomes_het=6772;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255302;ANN=TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|248/7088|135/5592||-2508|,TCTATCTATCTACCTAC|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2509_-7-2508insGTAGGTAGATAGATAG|p.?|188/7028|-7/5451||-2508|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|242/3696|135/2100||-2508|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|248/7151|135/5655||-2508| GT:AD:DP:GQ 0/1:9:20:48 -17 41261233 . C T . . gnomad_exomes_an=31268;gnomad_exomes_hom=1604;gnomad_exomes_het=6702;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191449;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-2683G>A|p.?|248/7088|135/5592||-2682|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2683G>A|p.?|188/7028|-7/5451||-2682|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2683G>A|p.?|242/3696|135/2100||-2682|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2683G>A|p.?|248/7151|135/5655||-2682| GT:AD:DP:GQ 0/1:12:27:48 -17 41263044 . A G . . gnomad_exomes_an=30560;gnomad_exomes_hom=1541;gnomad_exomes_het=6552;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191458;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-4494T>C|p.?|248/7088|135/5592||-4493|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-4494T>C|p.?|188/7028|-7/5451||-4493|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-4494T>C|p.?|242/3696|135/2100||-4493|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-4494T>C|p.?|248/7151|135/5655||-4493| GT:AD:DP:GQ 0/1:7:14:48 -17 41263117 . C CA . . gnomad_exomes_an=17480;gnomad_exomes_hom=629;gnomad_exomes_het=3959;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-4568_135-4567insT|p.?|248/7088|135/5592||-4567|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-4568_-7-4567insT|p.?|188/7028|-7/5451||-4567|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-4568_135-4567insT|p.?|242/3696|135/2100||-4567|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-4568_135-4567insT|p.?|248/7151|135/5655||-4567| GT:AD:DP:GQ 0/1:13:23:34 -17 41263566 . T C . . gnomad_exomes_an=29818;gnomad_exomes_hom=1603;gnomad_exomes_het=6680;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191462;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+4177A>G|p.?|247/7088|134/5592||4176|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5016A>G|p.?|188/7028|-7/5451||-5015|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+4177A>G|p.?|241/3696|134/2100||4176|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+4177A>G|p.?|247/7151|134/5655||4176| GT:AD:DP:GQ 0/1:11:19:48 -17 41264146 . G A . . gnomad_exomes_an=30782;gnomad_exomes_hom=1483;gnomad_exomes_het=6307;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191465;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+3597C>T|p.?|247/7088|134/5592||3596|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5596C>T|p.?|188/7028|-7/5451||-5595|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3597C>T|p.?|241/3696|134/2100||3596|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3597C>T|p.?|247/7151|134/5655||3596| GT:AD:DP:GQ 0/1:13:20:45 -17 41264364 . A G . . gnomad_exomes_an=31320;gnomad_exomes_hom=1500;gnomad_exomes_het=6409;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191467;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+3379T>C|p.?|247/7088|134/5592||3378|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5814T>C|p.?|188/7028|-7/5451||-5813|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3379T>C|p.?|241/3696|134/2100||3378|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3379T>C|p.?|247/7151|134/5655||3378| GT:AD:DP:GQ 0/1:8:24:45 -17 41264739 . C T . . gnomad_exomes_an=30908;gnomad_exomes_hom=3162;gnomad_exomes_het=7226;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255084;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+3004G>A|p.?|247/7088|134/5592||3003|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6189G>A|p.?|188/7028|-7/5451||-6188|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3004G>A|p.?|241/3696|134/2100||3003|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3004G>A|p.?|247/7151|134/5655||3003| GT:AD:DP:GQ:PS 0|1:14:29:48:41264739 -17 41264740 . TGA T . . gnomad_exomes_an=31014;gnomad_exomes_hom=3159;gnomad_exomes_het=7229;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+3001_134+3002delTC|p.?|247/7088|134/5592||3000|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6192_-7-6191delTC|p.?|188/7028|-7/5451||-6190|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3001_134+3002delTC|p.?|241/3696|134/2100||3000|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3001_134+3002delTC|p.?|247/7151|134/5655||3000| GT:AD:DP:GQ 0/1:14:30:48 -17 41264743 . CT C . . gnomad_exomes_an=30890;gnomad_exomes_hom=3155;gnomad_exomes_het=7228;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2999delA|p.?|247/7088|134/5592||2998|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6194delA|p.?|188/7028|-7/5451||-6193|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2999delA|p.?|241/3696|134/2100||2998|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2999delA|p.?|247/7151|134/5655||2998| GT:AD:DP:GQ:PS 0|1:14:29:48:41264739 -17 41264749 . C G . . gnomad_exomes_an=30892;gnomad_exomes_hom=3135;gnomad_exomes_het=7223;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000256095;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2994G>C|p.?|247/7088|134/5592||2993|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6199G>C|p.?|188/7028|-7/5451||-6198|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2994G>C|p.?|241/3696|134/2100||2993|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2994G>C|p.?|247/7151|134/5655||2993| GT:AD:DP:GQ:PS 0|1:14:29:48:41264739 -17 41264750 . A T . . gnomad_exomes_an=30880;gnomad_exomes_hom=3136;gnomad_exomes_het=7219;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255162;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2993T>A|p.?|247/7088|134/5592||2992|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6200T>A|p.?|188/7028|-7/5451||-6199|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2993T>A|p.?|241/3696|134/2100||2992|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2993T>A|p.?|247/7151|134/5655||2992| GT:AD:DP:GQ:PS 0|1:14:29:48:41264739 -17 41264751 . A AGGG . . gnomad_exomes_an=30776;gnomad_exomes_hom=3136;gnomad_exomes_het=7222;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2991_134+2992insCCC|p.?|247/7088|134/5592||2991|,AGGG|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6202_-7-6201insCCC|p.?|188/7028|-7/5451||-6201|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2991_134+2992insCCC|p.?|241/3696|134/2100||2991|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2991_134+2992insCCC|p.?|247/7151|134/5655||2991| GT:AD:DP:GQ:PS 0|1:14:29:48:41264739 -17 41264753 . C T . . gnomad_exomes_an=30714;gnomad_exomes_hom=3130;gnomad_exomes_het=7189;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255582;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2990G>A|p.?|247/7088|134/5592||2989|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6203G>A|p.?|188/7028|-7/5451||-6202|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2990G>A|p.?|241/3696|134/2100||2989|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2990G>A|p.?|247/7151|134/5655||2989| GT:AD:DP:GQ:PS 0|1:14:27:48:41264739 -17 41264755 . TGAAAC T . . gnomad_exomes_an=30768;gnomad_exomes_hom=3130;gnomad_exomes_het=7187;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2983_134+2987delGTTTC|p.?|247/7088|134/5592||2982|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6210_-7-6206delGTTTC|p.?|188/7028|-7/5451||-6205|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2983_134+2987delGTTTC|p.?|241/3696|134/2100||2982|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2983_134+2987delGTTTC|p.?|247/7151|134/5655||2982| GT:AD:DP:GQ:PS 0|1:14:27:48:41264739 -17 41265776 . A G . . gnomad_exomes_an=31332;gnomad_exomes_hom=1615;gnomad_exomes_het=6700;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191470;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+1967T>C|p.?|247/7088|134/5592||1966|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-7226T>C|p.?|188/7028|-7/5451||-7225|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+1967T>C|p.?|241/3696|134/2100||1966|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+1967T>C|p.?|247/7151|134/5655||1966| GT:AD:DP:GQ 0/1:23:37:44 -17 41266407 . C CT . . gnomad_exomes_an=22904;gnomad_exomes_hom=2326;gnomad_exomes_het=5197;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255595;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+1335_134+1336insA|p.?|247/7088|134/5592||1335|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-7858_-7-7857insA|p.?|188/7028|-7/5451||-7857|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+1335_134+1336insA|p.?|241/3696|134/2100||1335|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+1335_134+1336insA|p.?|247/7151|134/5655||1335| GT:AD:DP:GQ 0/1:10:18:33 -17 41267050 . G A . . gnomad_exomes_an=31332;gnomad_exomes_hom=1619;gnomad_exomes_het=6726;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191477;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+693C>T|p.?|247/7088|134/5592||692|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-8500C>T|p.?|188/7028|-7/5451||-8499|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+693C>T|p.?|241/3696|134/2100||692|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+693C>T|p.?|247/7151|134/5655||692| GT:AD:DP:GQ 0/1:7:23:44 -17 41267518 . CA C . . gnomad_exomes_an=21564;gnomad_exomes_hom=937;gnomad_exomes_het=6113;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+224delT|p.?|247/7088|134/5592||223|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+8515delT|p.?|187/7028|-8/5451||8514|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+224delT|p.?|241/3696|134/2100||223|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+224delT|p.?|247/7151|134/5655||223| GT:AD:DP:GQ 0/1:11:19:35 -17 41268206 . A C . . gnomad_exomes_an=31210;gnomad_exomes_hom=1544;gnomad_exomes_het=6707;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191483;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-410T>G|p.?|194/7088|81/5592||-409|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+7828T>G|p.?|187/7028|-8/5451||7827|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-410T>G|p.?|188/3696|81/2100||-409|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-410T>G|p.?|194/7151|81/5655||-409| GT:AD:DP:GQ:PS 0|1:13:22:46:41268206 -17 41268208 . C CT . . gnomad_exomes_an=31128;gnomad_exomes_hom=1385;gnomad_exomes_het=6554;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255730;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-413_81-412insA|p.?|194/7088|81/5592||-412|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+7825_-8+7826insA|p.?|187/7028|-8/5451||7825|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-413_81-412insA|p.?|188/3696|81/2100||-412|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-413_81-412insA|p.?|194/7151|81/5655||-412| GT:AD:DP:GQ:PS 0|1:13:22:46:41268206 -17 41270229 . T G . . gnomad_exomes_an=31274;gnomad_exomes_hom=1606;gnomad_exomes_het=6696;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191491;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-2433A>C|p.?|194/7088|81/5592||-2432|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5805A>C|p.?|187/7028|-8/5451||5804|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2433A>C|p.?|188/3696|81/2100||-2432|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2433A>C|p.?|194/7151|81/5655||-2432| GT:AD:DP:GQ 0/1:7:24:40 -17 41270277 . C T . . gnomad_exomes_an=31338;gnomad_exomes_hom=1513;gnomad_exomes_het=6416;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191493;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-2481G>A|p.?|194/7088|81/5592||-2480|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5757G>A|p.?|187/7028|-8/5451||5756|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2481G>A|p.?|188/3696|81/2100||-2480|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2481G>A|p.?|194/7151|81/5655||-2480| GT:AD:DP:GQ 0/1:9:22:48 -17 41270463 . G A . . gnomad_exomes_an=30876;gnomad_exomes_hom=1578;gnomad_exomes_het=6604;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191497;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-2667C>T|p.?|194/7088|81/5592||-2666|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5571C>T|p.?|187/7028|-8/5451||5570|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2667C>T|p.?|188/3696|81/2100||-2666|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2667C>T|p.?|194/7151|81/5655||-2666| GT:AD:DP:GQ 0/1:15:28:48 -17 41270666 . C A . . gnomad_exomes_an=31306;gnomad_exomes_hom=1500;gnomad_exomes_het=6413;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191498;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-2870G>T|p.?|194/7088|81/5592||-2869|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5368G>T|p.?|187/7028|-8/5451||5367|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2870G>T|p.?|188/3696|81/2100||-2869|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2870G>T|p.?|194/7151|81/5655||-2869| GT:AD:DP:GQ 0/1:11:15:43 -17 41270778 . C CT . . gnomad_exomes_an=23434;gnomad_exomes_hom=923;gnomad_exomes_het=4562;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000256051;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-2983_81-2982insA|p.?|194/7088|81/5592||-2982|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5255_-8+5256insA|p.?|187/7028|-8/5451||5255|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2983_81-2982insA|p.?|188/3696|81/2100||-2982|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2983_81-2982insA|p.?|194/7151|81/5655||-2982| GT:AD:DP:GQ 0/1:11:16:14 -17 41271293 . GA G . . gnomad_exomes_an=26204;gnomad_exomes_hom=4218;gnomad_exomes_het=6049;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-3498delT|p.?|194/7088|81/5592||-3497|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+4740delT|p.?|187/7028|-8/5451||4739|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-3498delT|p.?|188/3696|81/2100||-3497|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-3498delT|p.?|194/7151|81/5655||-3497| GT:AD:DP:GQ 0/1:10:20:48 -17 41273095 . G A . . gnomad_exomes_an=27498;gnomad_exomes_hom=1472;gnomad_exomes_het=6401;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191505;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2939C>T|p.?|193/7088|80/5592||2938|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2939C>T|p.?|187/7028|-8/5451||2938|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2939C>T|p.?|187/3696|80/2100||2938|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2939C>T|p.?|193/7151|80/5655||2938| GT:AD:DP:GQ 0/1:12:20:47 -17 41273348 . T C . . gnomad_exomes_an=31018;gnomad_exomes_hom=4264;gnomad_exomes_het=6559;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191507;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2686A>G|p.?|193/7088|80/5592||2685|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2686A>G|p.?|187/7028|-8/5451||2685|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2686A>G|p.?|187/3696|80/2100||2685|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2686A>G|p.?|193/7151|80/5655||2685| GT:AD:DP:GQ 0/1:18:31:47 -17 41273379 . G C . . gnomad_exomes_an=30948;gnomad_exomes_hom=1487;gnomad_exomes_het=6371;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191508;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2655C>G|p.?|193/7088|80/5592||2654|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2655C>G|p.?|187/7028|-8/5451||2654|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2655C>G|p.?|187/3696|80/2100||2654|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2655C>G|p.?|193/7151|80/5655||2654| GT:AD:DP:GQ 0/1:19:33:47 -17 41273537 . A C . . gnomad_exomes_an=30662;gnomad_exomes_hom=1552;gnomad_exomes_het=6479;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191510;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2497T>G|p.?|193/7088|80/5592||2496|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2497T>G|p.?|187/7028|-8/5451||2496|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2497T>G|p.?|187/3696|80/2100||2496|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2497T>G|p.?|193/7151|80/5655||2496| GT:AD:DP:GQ 0/1:14:33:48 -17 41274778 . G A . . gnomad_exomes_an=31152;gnomad_exomes_hom=1594;gnomad_exomes_het=6661;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191511;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+1256C>T|p.?|193/7088|80/5592||1255|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+1256C>T|p.?|187/7028|-8/5451||1255|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+1256C>T|p.?|187/3696|80/2100||1255|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+1256C>T|p.?|193/7151|80/5655||1255| GT:AD:DP:GQ 0/1:11:27:48 -17 41274906 . G A . . gnomad_exomes_an=28872;gnomad_exomes_hom=3662;gnomad_exomes_het=6225;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191514;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+1128C>T|p.?|193/7088|80/5592||1127|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+1128C>T|p.?|187/7028|-8/5451||1127|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+1128C>T|p.?|187/3696|80/2100||1127|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+1128C>T|p.?|193/7151|80/5655||1127| GT:AD:DP:GQ 0/1:17:27:47 -17 41275081 . G GA . . gnomad_exomes_an=29534;gnomad_exomes_hom=1365;gnomad_exomes_het=6118;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191515;ANN=GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+952_80+953insT|p.?|193/7088|80/5592||952|,GA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+952_-8+953insT|p.?|187/7028|-8/5451||952|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+952_80+953insT|p.?|187/3696|80/2100||952|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+952_80+953insT|p.?|193/7151|80/5655||952| GT:AD:DP:GQ 0/1:10:22:47 -17 41275151 . G C . . gnomad_exomes_an=31080;gnomad_exomes_hom=1493;gnomad_exomes_het=6342;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191516;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+883C>G|p.?|193/7088|80/5592||882|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+883C>G|p.?|187/7028|-8/5451||882|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+883C>G|p.?|187/3696|80/2100||882|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+883C>G|p.?|193/7151|80/5655||882| GT:AD:DP:GQ 0/1:15:28:48 -17 41275366 . GTTTTTTT G . . ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+661_80+667delAAAAAAA|p.?|193/7088|80/5592||660|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+661_-8+667delAAAAAAA|p.?|187/7028|-8/5451||660|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+661_80+667delAAAAAAA|p.?|187/3696|80/2100||660|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+661_80+667delAAAAAAA|p.?|193/7151|80/5655||660| GT:AD:DP:GQ 0/1:10:21:48 -17 41275645 . A G . . gnomad_exomes_an=31292;gnomad_exomes_hom=1615;gnomad_exomes_het=6682;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001689724;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+389T>C|p.?|193/7088|80/5592||388|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+389T>C|p.?|187/7028|-8/5451||388|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+389T>C|p.?|187/3696|80/2100||388|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+389T>C|p.?|193/7151|80/5655||388| GT:AD:DP:GQ 0/1:15:32:48 -17 41276247 . A G . . gnomad_exomes_an=31318;gnomad_exomes_hom=1611;gnomad_exomes_het=6702;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001610389;ANN=G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|1/22|c.-19-115T>C|p.?|95/7088|-19/5592||-114|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-106-115T>C|p.?|89/7028|-106/5451||-114|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-19-115T>C|p.?|89/3696|-19/2100||-114|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-19-115T>C|p.?|95/7151|-19/5655||-114| GT:AD:DP:GQ 0/1:18:28:44 -17 41276348 . T C . . gnomad_exomes_an=31332;gnomad_exomes_hom=1609;gnomad_exomes_het=6706;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001711604;ANN=C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|1/22|c.-19-216A>G|p.?|95/7088|-19/5592||-215|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-106-216A>G|p.?|89/7028|-106/5451||-215|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-19-216A>G|p.?|89/3696|-19/2100||-215|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-19-216A>G|p.?|95/7151|-19/5655||-215| GT:AD:DP:GQ 0/1:17:30:47 -17 41277187 . G C . . gnomad_exomes_an=29432;gnomad_exomes_hom=4088;gnomad_exomes_het=6345;gnomad_genomes_an=128296;gnomad_genomes_hom=11705;gnomad_genomes_het=29182;clinvar_clinsig=benign;clinvar_rcv=RCV001711453;ANN=C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|1/22|c.-20+101C>G|p.?|94/7088|-20/5592||100|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-107+107C>G|p.?|88/7028|-107/5451||106|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-20+107C>G|p.?|88/3696|-20/2100||106|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-20+101C>G|p.?|94/7151|-20/5655||100| GT:AD:DP:GQ 0/1:14:28:48 -MT 152 . T C . . . GT:GQ:AD:DP 1/1:98.13:2:10584 -MT 263 . A G . . . GT:GQ:AD:DP 1/1:98.13:0:7628 -MT 302 . A AC . . . GT:GQ:AD:DP 1/1:96.52:40:3536 -MT 310 . T TC . . . GT:GQ:AD:DP 1/1:96.88:7:3742 -MT 310 . T C . . . GT:GQ:AD:DP 0/1:21.54:7:3742 -MT 539 . T A . . . GT:GQ:AD:DP 0/1:21.53:6115:6405 -MT 596 . T A . . . GT:GQ:AD:DP 0/1:17.66:7690:7850 -MT 605 . T A . . . GT:GQ:AD:DP 0/1:21.53:5916:6058 -MT 610 . T A . . . GT:GQ:AD:DP 0/1:3.4:5986:6129 -MT 616 . T A . . . GT:GQ:AD:DP 0/1:0.12:6178:6261 -MT 750 . A G . . . GT:GQ:AD:DP 1/1:98.13:1:7819 -MT 1438 . A G . . . GT:GQ:AD:DP 1/1:98.13:2:9170 -MT 2141 . T TAG . . . GT:GQ:AD:DP 0/1:20:6260:6286 -MT 2259 . C T . . . GT:GQ:AD:DP 1/1:98.13:3:7528 -MT 2645 . G A . . . GT:GQ:AD:DP 0/1:21.53:9159:9193 -MT 3572 . T G . . . GT:GQ:AD:DP 0/1:21.53:6937:7895 -MT 3572 . T A . . . GT:GQ:AD:DP 0/1:21.49:6937:7895 -MT 3577 . A C . . . GT:GQ:AD:DP 0/1:21.53:7519:7979 -MT 3578 . T A . . . GT:GQ:AD:DP 0/1:21.53:7041:7921 -MT 3578 . T G . . . GT:GQ:AD:DP 0/1:21.53:7041:7921 -MT 3583 . A C . . . GT:GQ:AD:DP 0/1:21.53:7746:8049 -MT 3590 . T A . . . GT:GQ:AD:DP 0/1:21.53:6859:7638 -MT 3593 . T G . . . GT:GQ:AD:DP 0/1:0.51:7844:8078 -MT 3595 . A C . . . GT:GQ:AD:DP 0/1:21.22:7958:8111 -MT 3599 . T A . . . GT:GQ:AD:DP 0/1:21.53:7408:7913 -MT 3605 . T A . . . GT:GQ:AD:DP 0/1:21.53:5371:5645 -MT 3614 . T A . . . GT:GQ:AD:DP 0/1:20.35:5553:5689 -MT 3631 . T A . . . GT:GQ:AD:DP 0/1:20.17:5740:5893 -MT 3633 . T A . . . GT:GQ:AD:DP 0/1:10.82:5829:5943 -MT 4434 . T G . . . GT:GQ:AD:DP 0/1:0.79:7711:7878 -MT 4491 . G A . . . GT:GQ:AD:DP 0/1:14.25:6096:6108 -MT 4745 . A G . . . GT:GQ:AD:DP:PS 1|1:94.1:0:4255:4745 -MT 4769 . A G . . . GT:GQ:AD:DP:PS 1|1:96.49:0:4115:4745 -MT 6518 . C T . . . GT:GQ:AD:DP 0/1:21.4:9464:9504 -MT 7337 . G A . . . GT:GQ:AD:DP 1/1:93.49:2:8855 -MT 8129 . A C . . . GT:GQ:AD:DP 0/1:20.26:7971:8173 -MT 8860 . A G . . . GT:GQ:AD:DP 1/1:91.87:0:4988 -MT 13326 . T C . . . GT:GQ:AD:DP 1/1:98.13:2:9163 -MT 13680 . C T . . . GT:GQ:AD:DP 1/1:98.13:1:5581 -MT 13680 . C G . . . GT:GQ:AD:DP 0/1:25.75:1:5581 -MT 13752 . T G . . . GT:GQ:AD:DP 0/1:21.51:4714:4779 -MT 13762 . T G . . . GT:GQ:AD:DP 0/1:21.53:4509:4689 -MT 13768 . T G . . . GT:GQ:AD:DP 0/1:21.53:4623:4778 -MT 13769 . T G . . . GT:GQ:AD:DP 0/1:21.53:4684:4799 -MT 14831 . G A . . . GT:GQ:AD:DP 1/1:98.13:3:8846 -MT 14831 . G C . . . GT:GQ:AD:DP 0/1:49.84:3:8846 -MT 14872 . C T . . . GT:GQ:AD:DP 1/1:98.13:5:6667 -MT 14918 . G A . . . GT:GQ:AD:DP 0/1:21.37:6570:6807 -MT 15326 . A G . . . GT:GQ:AD:DP 1/1:98.13:1:7648 -MT 16023 . G A . . . GT:GQ:AD:DP 0/1:51.92:2572:9277 +17 41244000 . T C . . gnomad_exomes_an=31346;gnomad_exomes_hom=1591;gnomad_exomes_het=6707;gnomad_genomes_an=250954;gnomad_genomes_hom=16402;gnomad_genomes_het=55703;clinvar_clinsig=benign;clinvar_rcv=RCV000112115;clinvar_vcv=VCV000041818;ANN=C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|10/23|c.3548A>G|p.K1183R|3661/7088|3548/5592|1183/1864|2878|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.3407A>G|p.K1136R|3601/7028|3407/5451|1136/1817|2878|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.788-951A>G|p.?|895/3696|788/2100||-950|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.3548A>G|p.K1183R|3661/7151|3548/5655|1183/1885|2878| GT:AD:DP:GQ 0/1:8,18:26:43 +17 41244435 . T C . . gnomad_exomes_an=31332;gnomad_exomes_hom=1505;gnomad_exomes_het=6415;gnomad_genomes_an=251032;gnomad_genomes_hom=16145;gnomad_genomes_het=55137;clinvar_clinsig=benign;clinvar_rcv=RCV000112006;clinvar_vcv=VCV000041815;ANN=C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|10/23|c.3113A>G|p.E1038G|3226/7088|3113/5592|1038/1864|2443|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2972A>G|p.E991G|3166/7028|2972/5451|991/1817|2443|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.788-1386A>G|p.?|895/3696|788/2100||-1385|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.3113A>G|p.E1038G|3226/7151|3113/5655|1038/1885|2443| GT:AD:DP:GQ 0/1:12,14:26:47 +17 41244936 . G A . . gnomad_exomes_an=31324;gnomad_exomes_hom=4287;gnomad_exomes_het=6594;gnomad_genomes_an=251034;gnomad_genomes_hom=22738;gnomad_genomes_het=55898;clinvar_clinsig=benign;clinvar_rcv=RCV000111903;clinvar_vcv=VCV000041812;ANN=A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|10/23|c.2612C>T|p.P871L|2725/7088|2612/5592|871/1864|1942|,A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2471C>T|p.P824L|2665/7028|2471/5451|824/1817|1942|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1825C>T|p.?|894/3696|787/2100||1824|,A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2612C>T|p.P871L|2725/7151|2612/5655|871/1885|1942| GT:AD:DP:GQ 0/1:17,13:30:47 +17 41245237 . A G . . gnomad_exomes_an=31314;gnomad_exomes_hom=1492;gnomad_exomes_het=6416;gnomad_genomes_an=250946;gnomad_genomes_hom=16057;gnomad_genomes_het=55063;clinvar_clinsig=benign;clinvar_rcv=RCV000111822;clinvar_vcv=VCV000125554;ANN=G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|10/23|c.2311T>C|p.L771=|2424/7088|2311/5592|771/1864|-1786|,G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2170T>C|p.L724=|2364/7028|2170/5451|724/1817|-1786|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1524T>C|p.?|894/3696|787/2100||1523|,G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2311T>C|p.L771=|2424/7151|2311/5655|771/1885|-1786| GT:AD:DP:GQ 0/1:18,11:29:46 +17 41245466 . G A . . gnomad_exomes_an=31338;gnomad_exomes_hom=1602;gnomad_exomes_het=6709;gnomad_genomes_an=251110;gnomad_genomes_hom=16420;gnomad_genomes_het=55707;clinvar_clinsig=benign;clinvar_rcv=RCV000111763;clinvar_vcv=VCV000125536;ANN=A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|10/23|c.2082C>T|p.S694=|2195/7088|2082/5592|694/1864|-2015|,A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.1941C>T|p.S647=|2135/7028|1941/5451|647/1817|-2015|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1295C>T|p.?|894/3696|787/2100||1294|,A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2082C>T|p.S694=|2195/7151|2082/5655|694/1885|-2015| GT:AD:DP:GQ 0/1:11,8:19:48 +17 41247122 . A ACCT . . gnomad_exomes_an=31242;gnomad_exomes_hom=1750;gnomad_exomes_het=7017;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191391;clinvar_vcv=VCV000127125;ANN=ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|9/22|c.671-246_671-245insAGG|p.?|784/7088|671/5592||-245|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|8/21|c.530-246_530-245insAGG|p.?|724/7028|530/5451||-245|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|9/21|c.671-246_671-245insAGG|p.?|778/3696|671/2100||-245|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|9/23|c.671-246_671-245insAGG|p.?|784/7151|671/5655||-245| GT:AD:DP:GQ 0/1:18,11:29:45 +17 41247604 . A C . . gnomad_exomes_an=30832;gnomad_exomes_hom=1544;gnomad_exomes_het=6574;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191392;clinvar_vcv=VCV000209447;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|9/22|c.670+259T>G|p.?|783/7088|670/5592||258|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|8/21|c.529+259T>G|p.?|723/7028|529/5451||258|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|9/21|c.670+259T>G|p.?|777/3696|670/2100||258|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|9/23|c.670+259T>G|p.?|783/7151|670/5655||258| GT:AD:DP:GQ 0/1:12,11:23:47 +17 41248164 . C T . . gnomad_exomes_an=31116;gnomad_exomes_hom=1468;gnomad_exomes_het=6372;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191394;clinvar_vcv=VCV000209449;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/22|c.594-225G>A|p.?|707/7088|594/5592||-224|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-225G>A|p.?|647/7028|453/5451||-224|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-225G>A|p.?|701/3696|594/2100||-224|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-225G>A|p.?|707/7151|594/5655||-224| GT:AD:DP:GQ 0/1:14,7:21:44 +17 41248393 . C CAAAAAAAAAA . . ANN=CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/22|c.594-455_594-454insTTTTTTTTTT|p.?|707/7088|594/5592||-454|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-455_453-454insTTTTTTTTTT|p.?|647/7028|453/5451||-454|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-455_594-454insTTTTTTTTTT|p.?|701/3696|594/2100||-454|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-455_594-454insTTTTTTTTTT|p.?|707/7151|594/5655||-454| GT:AD:DP:GQ 0/1:9,7:16:48 +17 41248484 . G C . . gnomad_exomes_an=30426;gnomad_exomes_hom=1385;gnomad_exomes_het=6148;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191395;clinvar_vcv=VCV000209450;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/22|c.594-545C>G|p.?|707/7088|594/5592||-544|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-545C>G|p.?|647/7028|453/5451||-544|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-545C>G|p.?|701/3696|594/2100||-544|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-545C>G|p.?|707/7151|594/5655||-544| GT:AD:DP:GQ 0/1:11,9:20:48 +17 41248588 . CA C . . gnomad_exomes_an=12806;gnomad_exomes_hom=585;gnomad_exomes_het=4704;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/22|c.594-650delT|p.?|707/7088|594/5592||-649|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-650delT|p.?|647/7028|453/5451||-649|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-650delT|p.?|701/3696|594/2100||-649|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-650delT|p.?|707/7151|594/5655||-649| GT:AD:DP:GQ 0/1:9,10:19:42 +17 41249094 . A G . . gnomad_exomes_an=31332;gnomad_exomes_hom=1602;gnomad_exomes_het=6703;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191396;clinvar_vcv=VCV000209451;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/22|c.593+167T>C|p.?|706/7088|593/5592||166|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.452+167T>C|p.?|646/7028|452/5451||166|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.593+167T>C|p.?|700/3696|593/2100||166|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.593+167T>C|p.?|706/7151|593/5655||166| GT:AD:DP:GQ 0/1:9,7:16:48 +17 41249363 . TA T . . gnomad_exomes_an=31286;gnomad_exomes_hom=1497;gnomad_exomes_het=6409;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.548-58delT|p.?|661/7088|548/5592||-57|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.407-58delT|p.?|601/7028|407/5451||-57|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.548-58delT|p.?|655/3696|548/2100||-57|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.548-58delT|p.?|661/7151|548/5655||-57| GT:AD:DP:GQ 0/1:12,13:25:48 +17 41250047 . C CT . . gnomad_exomes_an=22188;gnomad_exomes_hom=992;gnomad_exomes_het=4281;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.548-742_548-741insA|p.?|661/7088|548/5592||-741|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.407-742_407-741insA|p.?|601/7028|407/5451||-741|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.548-742_548-741insA|p.?|655/3696|548/2100||-741|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.548-742_548-741insA|p.?|661/7151|548/5655||-741| GT:AD:DP:GQ 0/1:13,7:20:18 +17 41250678 . C CT . . gnomad_exomes_an=31058;gnomad_exomes_hom=1566;gnomad_exomes_het=6658;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191403;clinvar_vcv=VCV000209458;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.547+1113_547+1114insA|p.?|660/7088|547/5592||1113|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+1113_406+1114insA|p.?|600/7028|406/5451||1113|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+1113_547+1114insA|p.?|654/3696|547/2100||1113|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+1113_547+1114insA|p.?|660/7151|547/5655||1113| GT:AD:DP:GQ 0/1:6,16:22:42 +17 41250923 . T C . . gnomad_exomes_an=29782;gnomad_exomes_hom=4187;gnomad_exomes_het=6234;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191405;clinvar_vcv=VCV000209460;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.547+869A>G|p.?|660/7088|547/5592||868|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+869A>G|p.?|600/7028|406/5451||868|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+869A>G|p.?|654/3696|547/2100||868|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+869A>G|p.?|660/7151|547/5655||868| GT:AD:DP:GQ 0/1:13,9:22:47 +17 41251495 . C G . . gnomad_exomes_an=30850;gnomad_exomes_hom=1491;gnomad_exomes_het=6363;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191408;clinvar_vcv=VCV000209463;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.547+297G>C|p.?|660/7088|547/5592||296|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+297G>C|p.?|600/7028|406/5451||296|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+297G>C|p.?|654/3696|547/2100||296|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+297G>C|p.?|660/7151|547/5655||296| GT:AD:DP:GQ 0/1:11,15:26:48 +17 41251646 . T A . . gnomad_exomes_an=31294;gnomad_exomes_hom=1592;gnomad_exomes_het=6693;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000112727;clinvar_vcv=VCV000125879;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.547+146A>T|p.?|660/7088|547/5592||145|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+146A>T|p.?|600/7028|406/5451||145|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+146A>T|p.?|654/3696|547/2100||145|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+146A>T|p.?|660/7151|547/5655||145| GT:AD:DP:GQ 0/1:11,8:19:48 +17 41252575 . G A . . gnomad_exomes_an=6888;gnomad_exomes_hom=193;gnomad_exomes_het=1277;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191411;clinvar_vcv=VCV000209466;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-678C>T|p.?|555/7088|442/5592||-677|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-678C>T|p.?|495/7028|301/5451||-677|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-678C>T|p.?|549/3696|442/2100||-677|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-678C>T|p.?|555/7151|442/5655||-677| GT:AD:DP:GQ:PS 1|1:0,3:3:5:41252575 +17 41252591 . C CAT . . gnomad_exomes_an=10332;gnomad_exomes_hom=95;gnomad_exomes_het=571;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-695_442-694insAT|p.?|555/7088|442/5592||-694|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-695_301-694insAT|p.?|495/7028|301/5451||-694|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-695_442-694insAT|p.?|549/3696|442/2100||-694|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-695_442-694insAT|p.?|555/7151|442/5655||-694| GT:AD:DP:GQ:PS 1|1:0,2:2:4:41252575 +17 41254174 . A G . . gnomad_exomes_an=30142;gnomad_exomes_hom=1576;gnomad_exomes_het=6550;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191423;clinvar_vcv=VCV000209478;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1965T>C|p.?|554/7088|441/5592||1964|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1965T>C|p.?|494/7028|300/5451||1964|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1965T>C|p.?|548/3696|441/2100||1964|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1965T>C|p.?|554/7151|441/5655||1964| GT:AD:DP:GQ 0/1:14,13:27:48 +17 41254374 . C CTTTTTTTT . . gnomad_exomes_an=15994;gnomad_exomes_hom=494;gnomad_exomes_het=1743;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1764_441+1765insAAAAAAAA|p.?|554/7088|441/5592||1764|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1764_300+1765insAAAAAAAA|p.?|494/7028|300/5451||1764|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1764_441+1765insAAAAAAAA|p.?|548/3696|441/2100||1764|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1764_441+1765insAAAAAAAA|p.?|554/7151|441/5655||1764| GT:AD:DP:GQ 0/1:6,7:13:48 +17 41254405 . C T . . gnomad_exomes_an=24316;gnomad_exomes_hom=1000;gnomad_exomes_het=4795;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000256092;clinvar_vcv=VCV000264778;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1734G>A|p.?|554/7088|441/5592||1733|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1734G>A|p.?|494/7028|300/5451||1733|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1734G>A|p.?|548/3696|441/2100||1733|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1734G>A|p.?|554/7151|441/5655||1733| GT:AD:DP:GQ 0/1:5,9:14:43 +17 41254486 . T G . . gnomad_exomes_an=30560;gnomad_exomes_hom=4284;gnomad_exomes_het=6345;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191424;clinvar_vcv=VCV000209479;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1653A>C|p.?|554/7088|441/5592||1652|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1653A>C|p.?|494/7028|300/5451||1652|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1653A>C|p.?|548/3696|441/2100||1652|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1653A>C|p.?|554/7151|441/5655||1652| GT:AD:DP:GQ 0/1:8,15:23:46 +17 41254965 . C CT . . gnomad_exomes_an=26726;gnomad_exomes_hom=2359;gnomad_exomes_het=6380;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255713;clinvar_vcv=VCV000264845;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1173_441+1174insA|p.?|554/7088|441/5592||1173|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1173_300+1174insA|p.?|494/7028|300/5451||1173|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1173_441+1174insA|p.?|548/3696|441/2100||1173|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1173_441+1174insA|p.?|554/7151|441/5655||1173| GT:AD:DP:GQ 0/1:14,8:22:22 +17 41255102 . A G . . gnomad_exomes_an=31104;gnomad_exomes_hom=1426;gnomad_exomes_het=6400;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191428;clinvar_vcv=VCV000209483;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1037T>C|p.?|554/7088|441/5592||1036|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1037T>C|p.?|494/7028|300/5451||1036|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1037T>C|p.?|548/3696|441/2100||1036|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1037T>C|p.?|554/7151|441/5655||1036| GT:AD:DP:GQ:PS 0|1:19,12:31:46:41255102 +17 41255111 . A T . . gnomad_exomes_an=31114;gnomad_exomes_hom=1530;gnomad_exomes_het=6684;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191429;clinvar_vcv=VCV000209484;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1028T>A|p.?|554/7088|441/5592||1027|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1028T>A|p.?|494/7028|300/5451||1027|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1028T>A|p.?|548/3696|441/2100||1027|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1028T>A|p.?|554/7151|441/5655||1027| GT:AD:DP:GQ:PS 0|1:19,12:31:46:41255102 +17 41256074 . CA C . . gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+64delT|p.?|554/7088|441/5592||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||63| GT:AD:DP:GQ:PS 0|1:11,6:17:43:41256074 +17 41256089 . AAAAAAAAAGAAAAG A . . gnomad_exomes_an=28388;gnomad_exomes_hom=1079;gnomad_exomes_het=5744;gnomad_genomes_an=167932;gnomad_genomes_hom=9911;gnomad_genomes_het=23697;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|554/7088|441/5592||35|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+36_300+49delCTTTTCTTTTTTTT|p.?|494/7028|300/5451||35|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|548/3696|441/2100||35|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|554/7151|441/5655||35| GT:AD:DP:GQ:PS 0|1:13,6:19:43:41256074 +17 41257134 . T C . . gnomad_exomes_an=31346;gnomad_exomes_hom=4418;gnomad_exomes_het=6505;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000112024;clinvar_vcv=VCV000125614;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|4/22|c.213-161A>G|p.?|326/7088|213/5592||-160|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.72-161A>G|p.?|266/7028|72/5451||-160|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.213-161A>G|p.?|320/3696|213/2100||-160|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.213-161A>G|p.?|326/7151|213/5655||-160| GT:AD:DP:GQ 0/1:14,15:29:48 +17 41257458 . A C . . gnomad_exomes_an=31258;gnomad_exomes_hom=1500;gnomad_exomes_het=6414;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191434;clinvar_vcv=VCV000209489;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|4/22|c.213-485T>G|p.?|326/7088|213/5592||-484|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.72-485T>G|p.?|266/7028|72/5451||-484|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.213-485T>G|p.?|320/3696|213/2100||-484|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.213-485T>G|p.?|326/7151|213/5655||-484| GT:AD:DP:GQ 0/1:11,15:26:48 +17 41258043 . C T . . gnomad_exomes_an=30426;gnomad_exomes_hom=1538;gnomad_exomes_het=6460;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191436;clinvar_vcv=VCV000209491;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|4/22|c.212+430G>A|p.?|325/7088|212/5592||429|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.71+430G>A|p.?|265/7028|71/5451||429|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.212+430G>A|p.?|319/3696|212/2100||429|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.212+430G>A|p.?|325/7151|212/5655||429| GT:AD:DP:GQ 0/1:14,13:27:48 +17 41258135 . T TA . . gnomad_exomes_an=20132;gnomad_exomes_hom=1;gnomad_exomes_het=267;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|4/22|c.212+337_212+338insT|p.?|325/7088|212/5592||337|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.71+337_71+338insT|p.?|265/7028|71/5451||337|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.212+337_212+338insT|p.?|319/3696|212/2100||337|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.212+337_212+338insT|p.?|325/7151|212/5655||337| GT:AD:DP:GQ 1/1:3,11:14:4 +17 41259049 . C T . . gnomad_exomes_an=30790;gnomad_exomes_hom=1585;gnomad_exomes_het=6633;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191440;clinvar_vcv=VCV000209494;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-499G>A|p.?|248/7088|135/5592||-498|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-499G>A|p.?|188/7028|-7/5451||-498|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-499G>A|p.?|242/3696|135/2100||-498|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-499G>A|p.?|248/7151|135/5655||-498| GT:AD:DP:GQ 0/1:8,8:16:48 +17 41259079 . A ATT . . gnomad_exomes_an=21472;gnomad_exomes_hom=898;gnomad_exomes_het=3635;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-530_135-529insAA|p.?|248/7088|135/5592||-529|,ATT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-530_-7-529insAA|p.?|188/7028|-7/5451||-529|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-530_135-529insAA|p.?|242/3696|135/2100||-529|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-530_135-529insAA|p.?|248/7151|135/5655||-529| GT:AD:DP:GQ 0/1:10,3:13:7 +17 41259113 . G A . . gnomad_exomes_an=26218;gnomad_exomes_hom=2;gnomad_exomes_het=204;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255936;clinvar_vcv=VCV000264811;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-563C>T|p.?|248/7088|135/5592||-562|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-563C>T|p.?|188/7028|-7/5451||-562|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-563C>T|p.?|242/3696|135/2100||-562|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-563C>T|p.?|248/7151|135/5655||-562| GT:AD:DP:GQ 0/1:11,8:19:48 +17 41260352 . C CA . . gnomad_exomes_an=19754;gnomad_exomes_hom=856;gnomad_exomes_het=4728;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255985;clinvar_vcv=VCV000264791;ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-1803_135-1802insT|p.?|248/7088|135/5592||-1802|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-1803_-7-1802insT|p.?|188/7028|-7/5451||-1802|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-1803_135-1802insT|p.?|242/3696|135/2100||-1802|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-1803_135-1802insT|p.?|248/7151|135/5655||-1802| GT:AD:DP:GQ 0/1:11,8:19:43 +17 41260723 . C CAAAAA . . ANN=CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-2174_135-2173insTTTTT|p.?|248/7088|135/5592||-2173|,CAAAAA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2174_-7-2173insTTTTT|p.?|188/7028|-7/5451||-2173|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2174_135-2173insTTTTT|p.?|242/3696|135/2100||-2173|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2174_135-2173insTTTTT|p.?|248/7151|135/5655||-2173| GT:AD:DP:GQ 0/1:1,1:2:20 +17 41260808 . A G . . gnomad_exomes_an=30782;gnomad_exomes_hom=1558;gnomad_exomes_het=6565;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191445;clinvar_vcv=VCV000209499;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-2258T>C|p.?|248/7088|135/5592||-2257|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2258T>C|p.?|188/7028|-7/5451||-2257|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2258T>C|p.?|242/3696|135/2100||-2257|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2258T>C|p.?|248/7151|135/5655||-2257| GT:AD:DP:GQ 0/1:12,3:15:32 +17 41261058 . T TCTATCTATCTACCTAC . . gnomad_exomes_an=31232;gnomad_exomes_hom=1461;gnomad_exomes_het=6772;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255302;clinvar_vcv=VCV000264813;ANN=TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|248/7088|135/5592||-2508|,TCTATCTATCTACCTAC|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2509_-7-2508insGTAGGTAGATAGATAG|p.?|188/7028|-7/5451||-2508|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|242/3696|135/2100||-2508|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|248/7151|135/5655||-2508| GT:AD:DP:GQ 0/1:9,11:20:48 +17 41261233 . C T . . gnomad_exomes_an=31268;gnomad_exomes_hom=1604;gnomad_exomes_het=6702;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191449;clinvar_vcv=VCV000209503;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-2683G>A|p.?|248/7088|135/5592||-2682|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2683G>A|p.?|188/7028|-7/5451||-2682|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2683G>A|p.?|242/3696|135/2100||-2682|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2683G>A|p.?|248/7151|135/5655||-2682| GT:AD:DP:GQ 0/1:12,15:27:48 +17 41263044 . A G . . gnomad_exomes_an=30560;gnomad_exomes_hom=1541;gnomad_exomes_het=6552;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191458;clinvar_vcv=VCV000209512;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-4494T>C|p.?|248/7088|135/5592||-4493|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-4494T>C|p.?|188/7028|-7/5451||-4493|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-4494T>C|p.?|242/3696|135/2100||-4493|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-4494T>C|p.?|248/7151|135/5655||-4493| GT:AD:DP:GQ 0/1:7,7:14:48 +17 41263117 . C CA . . gnomad_exomes_an=17480;gnomad_exomes_hom=629;gnomad_exomes_het=3959;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-4568_135-4567insT|p.?|248/7088|135/5592||-4567|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-4568_-7-4567insT|p.?|188/7028|-7/5451||-4567|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-4568_135-4567insT|p.?|242/3696|135/2100||-4567|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-4568_135-4567insT|p.?|248/7151|135/5655||-4567| GT:AD:DP:GQ 0/1:13,10:23:34 +17 41263566 . T C . . gnomad_exomes_an=29818;gnomad_exomes_hom=1603;gnomad_exomes_het=6680;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191462;clinvar_vcv=VCV000209516;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+4177A>G|p.?|247/7088|134/5592||4176|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5016A>G|p.?|188/7028|-7/5451||-5015|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+4177A>G|p.?|241/3696|134/2100||4176|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+4177A>G|p.?|247/7151|134/5655||4176| GT:AD:DP:GQ 0/1:11,8:19:48 +17 41264146 . G A . . gnomad_exomes_an=30782;gnomad_exomes_hom=1483;gnomad_exomes_het=6307;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191465;clinvar_vcv=VCV000209519;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+3597C>T|p.?|247/7088|134/5592||3596|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5596C>T|p.?|188/7028|-7/5451||-5595|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3597C>T|p.?|241/3696|134/2100||3596|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3597C>T|p.?|247/7151|134/5655||3596| GT:AD:DP:GQ 0/1:13,7:20:45 +17 41264364 . A G . . gnomad_exomes_an=31320;gnomad_exomes_hom=1500;gnomad_exomes_het=6409;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191467;clinvar_vcv=VCV000209521;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+3379T>C|p.?|247/7088|134/5592||3378|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5814T>C|p.?|188/7028|-7/5451||-5813|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3379T>C|p.?|241/3696|134/2100||3378|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3379T>C|p.?|247/7151|134/5655||3378| GT:AD:DP:GQ 0/1:8,16:24:45 +17 41264739 . C T . . gnomad_exomes_an=30908;gnomad_exomes_hom=3162;gnomad_exomes_het=7226;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255084;clinvar_vcv=VCV000264785;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+3004G>A|p.?|247/7088|134/5592||3003|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6189G>A|p.?|188/7028|-7/5451||-6188|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3004G>A|p.?|241/3696|134/2100||3003|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3004G>A|p.?|247/7151|134/5655||3003| GT:AD:DP:GQ:PS 0|1:14,15:29:48:41264739 +17 41264740 . TGA T . . gnomad_exomes_an=31014;gnomad_exomes_hom=3159;gnomad_exomes_het=7229;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+3001_134+3002delTC|p.?|247/7088|134/5592||3000|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6192_-7-6191delTC|p.?|188/7028|-7/5451||-6190|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3001_134+3002delTC|p.?|241/3696|134/2100||3000|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3001_134+3002delTC|p.?|247/7151|134/5655||3000| GT:AD:DP:GQ 0/1:14,16:30:48 +17 41264743 . CT C . . gnomad_exomes_an=30890;gnomad_exomes_hom=3155;gnomad_exomes_het=7228;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2999delA|p.?|247/7088|134/5592||2998|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6194delA|p.?|188/7028|-7/5451||-6193|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2999delA|p.?|241/3696|134/2100||2998|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2999delA|p.?|247/7151|134/5655||2998| GT:AD:DP:GQ:PS 0|1:14,15:29:48:41264739 +17 41264749 . C G . . gnomad_exomes_an=30892;gnomad_exomes_hom=3135;gnomad_exomes_het=7223;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000256095;clinvar_vcv=VCV000264823;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2994G>C|p.?|247/7088|134/5592||2993|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6199G>C|p.?|188/7028|-7/5451||-6198|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2994G>C|p.?|241/3696|134/2100||2993|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2994G>C|p.?|247/7151|134/5655||2993| GT:AD:DP:GQ:PS 0|1:14,15:29:48:41264739 +17 41264750 . A T . . gnomad_exomes_an=30880;gnomad_exomes_hom=3136;gnomad_exomes_het=7219;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255162;clinvar_vcv=VCV000264824;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2993T>A|p.?|247/7088|134/5592||2992|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6200T>A|p.?|188/7028|-7/5451||-6199|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2993T>A|p.?|241/3696|134/2100||2992|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2993T>A|p.?|247/7151|134/5655||2992| GT:AD:DP:GQ:PS 0|1:14,15:29:48:41264739 +17 41264751 . A AGGG . . gnomad_exomes_an=30776;gnomad_exomes_hom=3136;gnomad_exomes_het=7222;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2991_134+2992insCCC|p.?|247/7088|134/5592||2991|,AGGG|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6202_-7-6201insCCC|p.?|188/7028|-7/5451||-6201|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2991_134+2992insCCC|p.?|241/3696|134/2100||2991|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2991_134+2992insCCC|p.?|247/7151|134/5655||2991| GT:AD:DP:GQ:PS 0|1:14,15:29:48:41264739 +17 41264753 . C T . . gnomad_exomes_an=30714;gnomad_exomes_hom=3130;gnomad_exomes_het=7189;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255582;clinvar_vcv=VCV000264819;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2990G>A|p.?|247/7088|134/5592||2989|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6203G>A|p.?|188/7028|-7/5451||-6202|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2990G>A|p.?|241/3696|134/2100||2989|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2990G>A|p.?|247/7151|134/5655||2989| GT:AD:DP:GQ:PS 0|1:14,13:27:48:41264739 +17 41264755 . TGAAAC T . . gnomad_exomes_an=30768;gnomad_exomes_hom=3130;gnomad_exomes_het=7187;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2983_134+2987delGTTTC|p.?|247/7088|134/5592||2982|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6210_-7-6206delGTTTC|p.?|188/7028|-7/5451||-6205|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2983_134+2987delGTTTC|p.?|241/3696|134/2100||2982|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2983_134+2987delGTTTC|p.?|247/7151|134/5655||2982| GT:AD:DP:GQ:PS 0|1:14,13:27:48:41264739 +17 41265776 . A G . . gnomad_exomes_an=31332;gnomad_exomes_hom=1615;gnomad_exomes_het=6700;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191470;clinvar_vcv=VCV000209524;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+1967T>C|p.?|247/7088|134/5592||1966|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-7226T>C|p.?|188/7028|-7/5451||-7225|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+1967T>C|p.?|241/3696|134/2100||1966|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+1967T>C|p.?|247/7151|134/5655||1966| GT:AD:DP:GQ 0/1:23,14:37:44 +17 41266407 . C CT . . gnomad_exomes_an=22904;gnomad_exomes_hom=2326;gnomad_exomes_het=5197;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255595;clinvar_vcv=VCV000264777;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+1335_134+1336insA|p.?|247/7088|134/5592||1335|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-7858_-7-7857insA|p.?|188/7028|-7/5451||-7857|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+1335_134+1336insA|p.?|241/3696|134/2100||1335|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+1335_134+1336insA|p.?|247/7151|134/5655||1335| GT:AD:DP:GQ 0/1:10,8:18:33 +17 41267050 . G A . . gnomad_exomes_an=31332;gnomad_exomes_hom=1619;gnomad_exomes_het=6726;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191477;clinvar_vcv=VCV000209531;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+693C>T|p.?|247/7088|134/5592||692|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-8500C>T|p.?|188/7028|-7/5451||-8499|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+693C>T|p.?|241/3696|134/2100||692|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+693C>T|p.?|247/7151|134/5655||692| GT:AD:DP:GQ 0/1:7,16:23:44 +17 41267518 . CA C . . gnomad_exomes_an=21564;gnomad_exomes_hom=937;gnomad_exomes_het=6113;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+224delT|p.?|247/7088|134/5592||223|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+8515delT|p.?|187/7028|-8/5451||8514|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+224delT|p.?|241/3696|134/2100||223|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+224delT|p.?|247/7151|134/5655||223| GT:AD:DP:GQ 0/1:11,8:19:35 +17 41268206 . A C . . gnomad_exomes_an=31210;gnomad_exomes_hom=1544;gnomad_exomes_het=6707;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191483;clinvar_vcv=VCV000209537;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-410T>G|p.?|194/7088|81/5592||-409|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+7828T>G|p.?|187/7028|-8/5451||7827|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-410T>G|p.?|188/3696|81/2100||-409|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-410T>G|p.?|194/7151|81/5655||-409| GT:AD:DP:GQ:PS 0|1:13,9:22:46:41268206 +17 41268208 . C CT . . gnomad_exomes_an=31128;gnomad_exomes_hom=1385;gnomad_exomes_het=6554;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255730;clinvar_vcv=VCV000264808;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-413_81-412insA|p.?|194/7088|81/5592||-412|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+7825_-8+7826insA|p.?|187/7028|-8/5451||7825|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-413_81-412insA|p.?|188/3696|81/2100||-412|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-413_81-412insA|p.?|194/7151|81/5655||-412| GT:AD:DP:GQ:PS 0|1:13,9:22:46:41268206 +17 41270229 . T G . . gnomad_exomes_an=31274;gnomad_exomes_hom=1606;gnomad_exomes_het=6696;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191491;clinvar_vcv=VCV000209545;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-2433A>C|p.?|194/7088|81/5592||-2432|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5805A>C|p.?|187/7028|-8/5451||5804|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2433A>C|p.?|188/3696|81/2100||-2432|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2433A>C|p.?|194/7151|81/5655||-2432| GT:AD:DP:GQ 0/1:7,17:24:40 +17 41270277 . C T . . gnomad_exomes_an=31338;gnomad_exomes_hom=1513;gnomad_exomes_het=6416;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191493;clinvar_vcv=VCV000209547;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-2481G>A|p.?|194/7088|81/5592||-2480|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5757G>A|p.?|187/7028|-8/5451||5756|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2481G>A|p.?|188/3696|81/2100||-2480|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2481G>A|p.?|194/7151|81/5655||-2480| GT:AD:DP:GQ 0/1:9,13:22:48 +17 41270463 . G A . . gnomad_exomes_an=30876;gnomad_exomes_hom=1578;gnomad_exomes_het=6604;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191497;clinvar_vcv=VCV000209551;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-2667C>T|p.?|194/7088|81/5592||-2666|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5571C>T|p.?|187/7028|-8/5451||5570|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2667C>T|p.?|188/3696|81/2100||-2666|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2667C>T|p.?|194/7151|81/5655||-2666| GT:AD:DP:GQ 0/1:15,13:28:48 +17 41270666 . C A . . gnomad_exomes_an=31306;gnomad_exomes_hom=1500;gnomad_exomes_het=6413;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191498;clinvar_vcv=VCV000209552;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-2870G>T|p.?|194/7088|81/5592||-2869|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5368G>T|p.?|187/7028|-8/5451||5367|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2870G>T|p.?|188/3696|81/2100||-2869|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2870G>T|p.?|194/7151|81/5655||-2869| GT:AD:DP:GQ 0/1:11,4:15:43 +17 41270778 . C CT . . gnomad_exomes_an=23434;gnomad_exomes_hom=923;gnomad_exomes_het=4562;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000256051;clinvar_vcv=VCV000264797;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-2983_81-2982insA|p.?|194/7088|81/5592||-2982|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5255_-8+5256insA|p.?|187/7028|-8/5451||5255|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2983_81-2982insA|p.?|188/3696|81/2100||-2982|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2983_81-2982insA|p.?|194/7151|81/5655||-2982| GT:AD:DP:GQ 0/1:11,5:16:14 +17 41271293 . GA G . . gnomad_exomes_an=26204;gnomad_exomes_hom=4218;gnomad_exomes_het=6049;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-3498delT|p.?|194/7088|81/5592||-3497|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+4740delT|p.?|187/7028|-8/5451||4739|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-3498delT|p.?|188/3696|81/2100||-3497|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-3498delT|p.?|194/7151|81/5655||-3497| GT:AD:DP:GQ 0/1:10,10:20:48 +17 41273095 . G A . . gnomad_exomes_an=27498;gnomad_exomes_hom=1472;gnomad_exomes_het=6401;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191505;clinvar_vcv=VCV000209559;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2939C>T|p.?|193/7088|80/5592||2938|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2939C>T|p.?|187/7028|-8/5451||2938|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2939C>T|p.?|187/3696|80/2100||2938|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2939C>T|p.?|193/7151|80/5655||2938| GT:AD:DP:GQ 0/1:12,8:20:47 +17 41273348 . T C . . gnomad_exomes_an=31018;gnomad_exomes_hom=4264;gnomad_exomes_het=6559;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191507;clinvar_vcv=VCV000209561;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2686A>G|p.?|193/7088|80/5592||2685|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2686A>G|p.?|187/7028|-8/5451||2685|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2686A>G|p.?|187/3696|80/2100||2685|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2686A>G|p.?|193/7151|80/5655||2685| GT:AD:DP:GQ 0/1:18,13:31:47 +17 41273379 . G C . . gnomad_exomes_an=30948;gnomad_exomes_hom=1487;gnomad_exomes_het=6371;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191508;clinvar_vcv=VCV000209562;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2655C>G|p.?|193/7088|80/5592||2654|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2655C>G|p.?|187/7028|-8/5451||2654|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2655C>G|p.?|187/3696|80/2100||2654|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2655C>G|p.?|193/7151|80/5655||2654| GT:AD:DP:GQ 0/1:19,14:33:47 +17 41273537 . A C . . gnomad_exomes_an=30662;gnomad_exomes_hom=1552;gnomad_exomes_het=6479;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191510;clinvar_vcv=VCV000209564;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2497T>G|p.?|193/7088|80/5592||2496|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2497T>G|p.?|187/7028|-8/5451||2496|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2497T>G|p.?|187/3696|80/2100||2496|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2497T>G|p.?|193/7151|80/5655||2496| GT:AD:DP:GQ 0/1:14,19:33:48 +17 41274778 . G A . . gnomad_exomes_an=31152;gnomad_exomes_hom=1594;gnomad_exomes_het=6661;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191511;clinvar_vcv=VCV000209565;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+1256C>T|p.?|193/7088|80/5592||1255|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+1256C>T|p.?|187/7028|-8/5451||1255|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+1256C>T|p.?|187/3696|80/2100||1255|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+1256C>T|p.?|193/7151|80/5655||1255| GT:AD:DP:GQ 0/1:11,16:27:48 +17 41274906 . G A . . gnomad_exomes_an=28872;gnomad_exomes_hom=3662;gnomad_exomes_het=6225;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191514;clinvar_vcv=VCV000209568;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+1128C>T|p.?|193/7088|80/5592||1127|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+1128C>T|p.?|187/7028|-8/5451||1127|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+1128C>T|p.?|187/3696|80/2100||1127|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+1128C>T|p.?|193/7151|80/5655||1127| GT:AD:DP:GQ 0/1:17,10:27:47 +17 41275081 . G GA . . gnomad_exomes_an=29534;gnomad_exomes_hom=1365;gnomad_exomes_het=6118;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191515;clinvar_vcv=VCV000209569;ANN=GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+952_80+953insT|p.?|193/7088|80/5592||952|,GA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+952_-8+953insT|p.?|187/7028|-8/5451||952|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+952_80+953insT|p.?|187/3696|80/2100||952|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+952_80+953insT|p.?|193/7151|80/5655||952| GT:AD:DP:GQ 0/1:10,12:22:47 +17 41275151 . G C . . gnomad_exomes_an=31080;gnomad_exomes_hom=1493;gnomad_exomes_het=6342;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191516;clinvar_vcv=VCV000209570;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+883C>G|p.?|193/7088|80/5592||882|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+883C>G|p.?|187/7028|-8/5451||882|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+883C>G|p.?|187/3696|80/2100||882|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+883C>G|p.?|193/7151|80/5655||882| GT:AD:DP:GQ 0/1:15,13:28:48 +17 41275366 . GTTTTTTT G . . ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+661_80+667delAAAAAAA|p.?|193/7088|80/5592||660|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+661_-8+667delAAAAAAA|p.?|187/7028|-8/5451||660|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+661_80+667delAAAAAAA|p.?|187/3696|80/2100||660|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+661_80+667delAAAAAAA|p.?|193/7151|80/5655||660| GT:AD:DP:GQ 0/1:10,11:21:48 +17 41275645 . A G . . gnomad_exomes_an=31292;gnomad_exomes_hom=1615;gnomad_exomes_het=6682;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191517;clinvar_vcv=VCV000209571;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+389T>C|p.?|193/7088|80/5592||388|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+389T>C|p.?|187/7028|-8/5451||388|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+389T>C|p.?|187/3696|80/2100||388|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+389T>C|p.?|193/7151|80/5655||388| GT:AD:DP:GQ 0/1:15,17:32:48 +17 41276247 . A G . . gnomad_exomes_an=31318;gnomad_exomes_hom=1611;gnomad_exomes_het=6702;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000111495;clinvar_vcv=VCV000125468;ANN=G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|1/22|c.-19-115T>C|p.?|95/7088|-19/5592||-114|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-106-115T>C|p.?|89/7028|-106/5451||-114|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-19-115T>C|p.?|89/3696|-19/2100||-114|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-19-115T>C|p.?|95/7151|-19/5655||-114| GT:AD:DP:GQ 0/1:18,10:28:44 +17 41276348 . T C . . gnomad_exomes_an=31332;gnomad_exomes_hom=1609;gnomad_exomes_het=6706;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191520;clinvar_vcv=VCV000209574;ANN=C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|1/22|c.-19-216A>G|p.?|95/7088|-19/5592||-215|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-106-216A>G|p.?|89/7028|-106/5451||-215|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-19-216A>G|p.?|89/3696|-19/2100||-215|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-19-216A>G|p.?|95/7151|-19/5655||-215| GT:AD:DP:GQ 0/1:17,13:30:47 +17 41277187 . G C . . gnomad_exomes_an=29432;gnomad_exomes_hom=4088;gnomad_exomes_het=6345;gnomad_genomes_an=128296;gnomad_genomes_hom=11705;gnomad_genomes_het=29182;clinvar_clinsig=benign;clinvar_rcv=RCV000169537;clinvar_vcv=VCV000189123;ANN=C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|1/22|c.-20+101C>G|p.?|94/7088|-20/5592||100|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-107+107C>G|p.?|88/7028|-107/5451||106|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-20+107C>G|p.?|88/3696|-20/2100||106|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-20+101C>G|p.?|94/7151|-20/5655||100| GT:AD:DP:GQ 0/1:14,14:28:48 +MT 152 . T C . . . GT:GQ:AD:DP 1/1:98.13:2,10582:10584 +MT 263 . A G . . . GT:GQ:AD:DP 1/1:98.13:0,7628:7628 +MT 302 . A AC . . . GT:GQ:AD:DP 1/1:96.52:40,3496:3536 +MT 310 . T TC . . . GT:GQ:AD:DP 1/1:96.88:100,3642:3742 +MT 310 . T C . . . GT:GQ:AD:DP 0/1:21.54:3649,93:3742 +MT 539 . T A . . . GT:GQ:AD:DP 0/1:21.53:6115,290:6405 +MT 596 . T A . . . GT:GQ:AD:DP 0/1:17.66:7690,160:7850 +MT 605 . T A . . . GT:GQ:AD:DP 0/1:21.53:5916,142:6058 +MT 610 . T A . . . GT:GQ:AD:DP 0/1:3.4:5986,143:6129 +MT 616 . T A . . . GT:GQ:AD:DP 0/1:0.12:6178,83:6261 +MT 750 . A G . . . GT:GQ:AD:DP 1/1:98.13:1,7818:7819 +MT 1438 . A G . . . GT:GQ:AD:DP 1/1:98.13:2,9168:9170 +MT 2141 . T TAG . . . GT:GQ:AD:DP 0/1:20:6260,26:6286 +MT 2259 . C T . . . GT:GQ:AD:DP 1/1:98.13:3,7525:7528 +MT 2645 . G A . . . GT:GQ:AD:DP 0/1:21.53:9159,34:9193 +MT 3572 . T G . . . GT:GQ:AD:DP 0/1:21.53:7257,638:7895 +MT 3572 . T A . . . GT:GQ:AD:DP 0/1:21.49:7575,320:7895 +MT 3577 . A C . . . GT:GQ:AD:DP 0/1:21.53:7519,460:7979 +MT 3578 . T A . . . GT:GQ:AD:DP 0/1:21.53:7352,569:7921 +MT 3578 . T G . . . GT:GQ:AD:DP 0/1:21.53:7610,311:7921 +MT 3583 . A C . . . GT:GQ:AD:DP 0/1:21.53:7746,303:8049 +MT 3590 . T A . . . GT:GQ:AD:DP 0/1:21.53:6859,779:7638 +MT 3593 . T G . . . GT:GQ:AD:DP 0/1:0.51:7844,234:8078 +MT 3595 . A C . . . GT:GQ:AD:DP 0/1:21.22:7958,153:8111 +MT 3599 . T A . . . GT:GQ:AD:DP 0/1:21.53:7408,505:7913 +MT 3605 . T A . . . GT:GQ:AD:DP 0/1:21.53:5371,274:5645 +MT 3614 . T A . . . GT:GQ:AD:DP 0/1:20.35:5553,136:5689 +MT 3631 . T A . . . GT:GQ:AD:DP 0/1:20.17:5740,153:5893 +MT 3633 . T A . . . GT:GQ:AD:DP 0/1:10.82:5829,114:5943 +MT 4434 . T G . . . GT:GQ:AD:DP 0/1:0.79:7711,167:7878 +MT 4491 . G A . . . GT:GQ:AD:DP 0/1:14.25:6096,12:6108 +MT 4745 . A G . . . GT:GQ:AD:DP:PS 1|1:94.1:0,4255:4255:4745 +MT 4769 . A G . . . GT:GQ:AD:DP:PS 1|1:96.49:0,4115:4115:4745 +MT 6518 . C T . . . GT:GQ:AD:DP 0/1:21.4:9464,40:9504 +MT 7337 . G A . . . GT:GQ:AD:DP 1/1:93.49:2,8853:8855 +MT 8129 . A C . . . GT:GQ:AD:DP 0/1:20.26:7971,202:8173 +MT 8860 . A G . . . GT:GQ:AD:DP 1/1:91.87:0,4988:4988 +MT 13326 . T C . . . GT:GQ:AD:DP 1/1:98.13:2,9161:9163 +MT 13680 . C T . . . GT:GQ:AD:DP 1/1:98.13:25,5556:5581 +MT 13680 . C G . . . GT:GQ:AD:DP 0/1:25.75:5557,24:5581 +MT 13752 . T G . . . GT:GQ:AD:DP 0/1:21.51:4714,65:4779 +MT 13762 . T G . . . GT:GQ:AD:DP 0/1:21.53:4509,180:4689 +MT 13768 . T G . . . GT:GQ:AD:DP 0/1:21.53:4623,155:4778 +MT 13769 . T G . . . GT:GQ:AD:DP 0/1:21.53:4684,115:4799 +MT 14831 . G A . . . GT:GQ:AD:DP 1/1:98.13:17,8829:8846 +MT 14831 . G C . . . GT:GQ:AD:DP 0/1:49.84:8832,14:8846 +MT 14872 . C T . . . GT:GQ:AD:DP 1/1:98.13:5,6662:6667 +MT 14918 . G A . . . GT:GQ:AD:DP 0/1:21.37:6570,237:6807 +MT 15326 . A G . . . GT:GQ:AD:DP 1/1:98.13:1,7647:7648 +MT 16023 . G A . . . GT:GQ:AD:DP 0/1:51.92:2572,6705:9277 diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_4_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_4_vcf.snap index 544964c6..1ff8ed23 100644 --- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_4_vcf.snap +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_4_vcf.snap @@ -53,6 +53,6 @@ expression: "std::fs::read_to_string(&args.path_out)?" ##x-varfish-version= ##x-varfish-version= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 -17 41256074 . CA C . . gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+64delT|p.?|554/7088|441/5592||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||63| GT:AD:DP:GQ:PS 0|1:11:17:43:41256074 -MT 750 . A G . . . GT:GQ:AD:DP 1/1:98.13:1:7819 +17 41256074 . CA C . . gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+64delT|p.?|554/7088|441/5592||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||63| GT:AD:DP:GQ:PS 0|1:11,6:17:43:41256074 +MT 750 . A G . . . GT:GQ:AD:DP 1/1:98.13:1,7818:7819 diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_9_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_9_vcf.snap index 950fb054..e9ae14ae 100644 --- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_9_vcf.snap +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_9_vcf.snap @@ -53,6 +53,6 @@ expression: "std::fs::read_to_string(&args.path_out)?" ##x-varfish-version= ##x-varfish-version= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CASE -17 41256074 . CA C . . gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+64delT|p.?|554/7088|441/5592||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||63| GT:AD:DP:GQ:PS 0|1:18:32:47:41256074 -MT 750 . A G . . . GT:GQ:AD:DP 1/1:98.13:1:5608 +17 41256074 . CA C . . gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+64delT|p.?|554/7088|441/5592||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||63| GT:AD:DP:GQ:PS 0|1:18,14:32:47:41256074 +MT 750 . A G . . . GT:GQ:AD:DP 1/1:98.13:1,5607:5608 diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_3_7-0_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_3_7-0_vcf.snap index d589f943..2aac98f6 100644 --- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_3_7-0_vcf.snap +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_3_7-0_vcf.snap @@ -57,6 +57,6 @@ expression: "std::fs::read_to_string(&args.path_out)?" ##x-varfish-version= ##x-varfish-version= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Case_1_father-N1-DNA1-WGS1 Case_1_index-N1-DNA1-WGS1 Case_1_mother-N1-DNA1-WGS1 -17 41210126 . C CTAGCACTT . . gnomad_exomes_an=31272;gnomad_exomes_hom=0;gnomad_exomes_het=85;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|18/22|c.5194-975_5194-974insAAGTGCTA|p.?|5307/7088|5194/5592||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|17/21|c.5053-975_5053-974insAAGTGCTA|p.?|5247/7028|5053/5451||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|18/21|c.1882-975_1882-974insAAGTGCTA|p.?|1989/3696|1882/2100||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|19/23|c.5257-975_5257-974insAAGTGCTA|p.?|5370/7151|5257/5655||-974| GT:AD:DP:GQ 0/0:29:29:87 0/1:23:36:99 0/1:15:32:99 -MT 750 . A G . . . GT:AD:DP:GQ 1/1:0:2757:99 1/1:0:2392:99 1/1:0:1621:99 +17 41210126 . C CTAGCACTT . . gnomad_exomes_an=31272;gnomad_exomes_hom=0;gnomad_exomes_het=85;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|18/22|c.5194-975_5194-974insAAGTGCTA|p.?|5307/7088|5194/5592||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|17/21|c.5053-975_5053-974insAAGTGCTA|p.?|5247/7028|5053/5451||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|18/21|c.1882-975_1882-974insAAGTGCTA|p.?|1989/3696|1882/2100||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|19/23|c.5257-975_5257-974insAAGTGCTA|p.?|5370/7151|5257/5655||-974| GT:AD:DP:GQ 0/0:29,0:29:87 0/1:23,13:36:99 0/1:15,17:32:99 +MT 750 . A G . . . GT:AD:DP:GQ 1/1:0,2757:2757:99 1/1:0,2392:2392:99 1/1:0,1621:1621:99 diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_4_4_0_0_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_4_4_0_0_vcf.snap index 8047035f..bc0a877d 100644 --- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_4_4_0_0_vcf.snap +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_4_4_0_0_vcf.snap @@ -53,6 +53,6 @@ expression: "std::fs::read_to_string(&args.path_out)?" ##x-varfish-version= ##x-varfish-version= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CASE -17 41256074 . CA C . . gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+64delT|p.?|554/7088|441/5592||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||63| GT:AD:DP:GQ:PS 1|1:0:80:99:41256074 -MT 750 . A G . . . GT:AD:DP:GQ 1/1:0:35:99 +17 41256074 . CA C . . gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+64delT|p.?|554/7088|441/5592||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||63| GT:AD:DP:GQ:PS 1|1:0,80:80:99:41256074 +MT 750 . A G . . . GT:AD:DP:GQ 1/1:0,35:35:99 diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_gz.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_gz.snap index 9102671b..bdc2246a 100644 --- a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_gz.snap +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_gz.snap @@ -2,514 +2,547 @@ source: src/seqvars/ingest/mod.rs expression: "String::from_utf8_lossy(&buffer)" --- -0000: 1F 8B 08 00 00 00 00 00 00 FF CD 9D EB 73 DB 46 .............s.F -0016: 92 C0 3F 6B FF 0A 95 53 75 FB C1 16 3D EF 07 7D ..?k...Su...=..} -0032: F2 15 57 72 18 D7 C5 8E 57 E6 66 EF 3E B1 14 99 ..Wr....W.f.>... -0048: 71 54 6B 49 3E 49 C9 25 57 FC E3 AF E7 05 E2 D1 qTkI>I.%W....... -0064: 03 4A C2 00 15 EF DA 60 08 0C BA D1 F3 9B 66 4F .J.....`......fO -0080: CF 03 DF 7C F3 F3 E5 97 CD 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3D 33 E1 4F 6C AD .z.m.=..5.=3.Ol. +8432: 63 C5 1E 72 90 29 F9 8B C2 B5 9C 49 B6 70 8A 85 c..r.).....I.p.. +8448: 87 A4 CF E6 4B DE 67 18 9A 84 17 C8 67 D6 7A B0 ....K.g.....g.z. +8464: 59 15 64 59 E0 AE 1F A4 6C 8E E3 1F 52 1D 41 C3 Y.dY....l...R.A. +8480: 38 82 D4 84 CE B0 56 DF 33 54 C3 DC 1A 7F 7B 0E 8.....V.3T....{. +8496: 9F 96 FE 4F 18 AA 71 EE 58 7F DF 63 EF 58 ED AF ...O..q.X..c.X.. +8512: A1 45 D1 4C 5B F6 80 61 97 AB 19 A2 14 11 AA 2C .E.L[..a......., +8528: 34 DB 25 47 18 35 37 01 DA 66 C6 65 AD 9D 51 F7 4.%G.57..f.e..Q. +8544: 8F BC 3E 93 12 FD 1B ED 3B AE 18 08 B1 9D 7E C8 ..>.....;.....~. +8560: 88 2D 15 43 68 5B 9C 4A 44 2A F9 86 0F 19 0A A5 .-.Ch[.JD*...... +8576: F6 E5 FE 02 D0 8C 2D 1B BA 07 35 B4 E8 89 05 8C ......-...5..... +8592: B9 F8 D0 B4 02 FA E1 52 3C 6B 0D E2 85 3B C4 8B .......R>, + /// ClinVar database as annonars RocksDB. + pub clinvar_db: Arc>, + /// ClinVar metadata from annonars. + pub clinvar_meta: annonars::clinvar_minimal::cli::query::Meta, + /// dbSNP database as annonars RocksDB. + pub dbsnp_db: Arc>, + /// dbSNP metadata from annonars. + pub dbsnp_meta: annonars::dbsnp::cli::query::Meta, + /// CADD database as annonars RocksDB. + pub cadd_db: Arc>, + /// CADD metadata from annonars. + pub cadd_meta: annonars::tsv::cli::query::Meta, + /// Coding context for CADD. + pub cadd_ctx: annonars::tsv::coding::Context, + /// dbNSFP database as annonars RocksDB. + pub dbnsfp_db: Arc>, + /// dbNSFP metadata from annonars. + pub dbnsfp_meta: annonars::tsv::cli::query::Meta, + /// Coding context for dbNSFP. + pub dbnsfp_ctx: annonars::tsv::coding::Context, +} + +impl AnnonarsDbs { + /// Initialize from path that contains the annonars databases. + fn with_path>( + path: P, + genome_release: GenomeRelease, + ) -> Result { + let path_annonars = path.as_ref().join("annonars"); + let path_genome_release = path_annonars.join(path_component(genome_release)); + + macro_rules! open_rocksdb { + ($path_token:expr, $module:ident, $db_name:expr, $meta_name:expr) => {{ + let path: std::path::PathBuf = + path_genome_release.join($path_token).join("rocksdb"); + annonars::$module::cli::query::open_rocksdb(&path, $db_name, $meta_name).map_err( + |e| { + anyhow::anyhow!( + "problem opening {} metadata at {}: {}", + $db_name, + path.as_os_str().to_string_lossy(), + e + ) + }, + )? + }}; + } + + let (clinvar_db, clinvar_meta) = + open_rocksdb!("clinvar-minimal", clinvar_minimal, "clinvar", "meta"); + let (cadd_db, cadd_meta) = open_rocksdb!("cadd", tsv, "tsv_data", "meta"); + let (dbnsfp_db, dbnsfp_meta) = open_rocksdb!("dbnsfp", tsv, "tsv_data", "meta"); + let (dbsnp_db, dbsnp_meta) = open_rocksdb!("dbsnp", dbsnp, "dbsnp_data", "meta"); + + let dbnsfp_ctx = annonars::tsv::coding::Context::new( + dbnsfp_meta.db_infer_config.clone(), + dbnsfp_meta.db_schema.clone(), + ); + let cadd_ctx = annonars::tsv::coding::Context::new( + cadd_meta.db_infer_config.clone(), + cadd_meta.db_schema.clone(), + ); + + let path_rocksdb = path_annonars.join("genes").join("rocksdb"); + let genes_db = annonars::genes::cli::query::open_rocksdb(&path_rocksdb, "genes", "meta") + .map_err(|e| { + anyhow::anyhow!( + "problem opening genes metadata at {}: {}", + path_rocksdb.as_os_str().to_string_lossy(), + e + ) + })?; + + Ok(Self { + clinvar_db, + clinvar_meta, + dbsnp_db, + dbsnp_meta, + cadd_db, + cadd_meta, + cadd_ctx, + dbnsfp_db, + dbnsfp_meta, + dbnsfp_ctx, + genes_db, + }) + } +} + +/// Utility for sequence variant annotation with annonars. +pub struct Annotator { + /// Annonars database bundles. + pub annonars_dbs: AnnonarsDbs, +} + +impl Annotator { + /// Construct with path to annonars databases. + /// + /// # Errors + /// + /// If there is a problem opening the databases. + pub fn with_path>( + path: P, + genome_release: GenomeRelease, + ) -> Result { + let annonars_dbs = AnnonarsDbs::with_path(path.as_ref(), genome_release).map_err(|e| { + anyhow::anyhow!( + "problem opening annonars databases at {}: {}", + path.as_ref().as_os_str().to_string_lossy(), + e + ) + })?; + Ok(Self { annonars_dbs }) + } + + /// Query `genes` database for a given HGNC ID. + /// + /// # Errors + /// + /// If there is a problem querying the database. + pub fn query_genes( + &self, + hgnc_id: &str, + ) -> Result, anyhow::Error> { + let cf_data = self + .annonars_dbs + .genes_db + .cf_handle("genes") + .ok_or_else(|| anyhow::anyhow!("could not get genes column family"))?; + + let raw_value = self + .annonars_dbs + .genes_db + .get_cf(&cf_data, hgnc_id.as_bytes()) + .map_err(|e| { + anyhow::anyhow!( + "problem querying genes database for HGNC ID {}: {}", + hgnc_id, + e + ) + })?; + + raw_value + .map(|raw_value| { + annonars::genes::pbs::Record::decode(&mut std::io::Cursor::new(&raw_value)).map_err( + |e| { + anyhow::anyhow!( + "problem decoding record from genes database for HGNC ID {}: {}", + hgnc_id, + e + ) + }, + ) + }) + .transpose() + } + + /// Query `clinvar-minimal` database for a given variant. + /// + /// # Errors + /// + /// If there is a problem querying the database. + pub fn query_clinvar_minimal( + &self, + seqvar: &SequenceVariant, + ) -> Result, anyhow::Error> { + let cf_data = self + .annonars_dbs + .clinvar_db + .cf_handle("clinvar") + .ok_or_else(|| anyhow::anyhow!("could not get clinvar column family"))?; + + let variant = annonars::common::spdi::Var::new( + annonars::common::cli::canonicalize(&seqvar.chrom), + seqvar.pos, + seqvar.reference.clone(), + seqvar.alternative.clone(), + ); + + annonars::clinvar_minimal::cli::query::query_for_variant( + &variant, + &self.annonars_dbs.clinvar_meta, + &self.annonars_dbs.clinvar_db, + &cf_data, + ) + .map_err(|e| anyhow::anyhow!("problem querying clinvar-minimal database: {}", e)) + } + + /// Query `dbsnp` database for a given variant. + /// + /// # Errors + /// + /// If there is a problem querying the database. + pub fn query_dbsnp( + &self, + seqvar: &SequenceVariant, + ) -> Result, anyhow::Error> { + let cf_data = self + .annonars_dbs + .dbsnp_db + .cf_handle("dbsnp_data") + .ok_or_else(|| anyhow::anyhow!("could not get dbsnp_data column family"))?; + + let variant = annonars::common::spdi::Var::new( + annonars::common::cli::canonicalize(&seqvar.chrom), + seqvar.pos, + seqvar.reference.clone(), + seqvar.alternative.clone(), + ); + + annonars::dbsnp::cli::query::query_for_variant( + &variant, + &self.annonars_dbs.dbsnp_meta, + &self.annonars_dbs.dbsnp_db, + &cf_data, + ) + .map_err(|e| anyhow::anyhow!("problem querying dbsnp database: {}", e)) + } + + /// Query `cadd` database for a given variant. + /// + /// # Errors + /// + /// If there is a problem querying the database. + pub fn query_cadd( + &self, + seqvar: &SequenceVariant, + ) -> Result>, anyhow::Error> { + let cf_data = self + .annonars_dbs + .cadd_db + .cf_handle("tsv_data") + .ok_or_else(|| anyhow::anyhow!("could not get tsv_data column family"))?; + + let variant = annonars::common::spdi::Var::new( + annonars::common::cli::canonicalize(&seqvar.chrom), + seqvar.pos, + seqvar.reference.clone(), + seqvar.alternative.clone(), + ); + + let values = annonars::tsv::cli::query::query_for_variant( + &variant, + &self.annonars_dbs.cadd_meta, + &self.annonars_dbs.cadd_db, + &cf_data, + &self.annonars_dbs.cadd_ctx, + ) + .map_err(|e| anyhow::anyhow!("problem querying CADD database: {}", e))?; + + Ok(values) + } + + /// Query `dbNSFP` database for a given variant. + /// + /// # Errors + /// + /// If there is a problem querying the database. + pub fn query_dbnsfp( + &self, + seqvar: &SequenceVariant, + ) -> Result>, anyhow::Error> { + let cf_data = self + .annonars_dbs + .dbnsfp_db + .cf_handle("tsv_data") + .ok_or_else(|| anyhow::anyhow!("could not get tsv_data column family"))?; + + let variant = annonars::common::spdi::Var::new( + annonars::common::cli::canonicalize(&seqvar.chrom), + seqvar.pos, + seqvar.reference.clone(), + seqvar.alternative.clone(), + ); + + let values = annonars::tsv::cli::query::query_for_variant( + &variant, + &self.annonars_dbs.dbnsfp_meta, + &self.annonars_dbs.dbnsfp_db, + &cf_data, + &self.annonars_dbs.dbnsfp_ctx, + ) + .map_err(|e| anyhow::anyhow!("problem querying dbNSFP database: {}", e))?; + + Ok(values) + } +} diff --git a/src/seqvars/query/interpreter/clinvar.rs b/src/seqvars/query/interpreter/clinvar.rs new file mode 100644 index 00000000..9f4b7250 --- /dev/null +++ b/src/seqvars/query/interpreter/clinvar.rs @@ -0,0 +1,50 @@ +use crate::seqvars::query::{ + annonars::Annotator, + schema::{CaseQuery, SequenceVariant}, +}; + +use annonars::clinvar_minimal::pbs::{self, ClinicalSignificance::*}; + +/// Determine whether the `SequenceVariant` passes the clinvar filter. +pub fn passes( + query: &CaseQuery, + annotator: &Annotator, + seqvar: &SequenceVariant, +) -> Result { + if !query.require_in_clinvar { + return Ok(true); + } + + if let Some(record) = annotator + .query_clinvar_minimal(seqvar) + .map_err(|e| anyhow::anyhow!("problem querying clinvar-minimal: {}", e))? + { + if let Some(assertion) = record.reference_assertions.first() { + let clinical_significance: pbs::ClinicalSignificance = assertion + .clinical_significance + .try_into() + .map_err(|e| anyhow::anyhow!("could not convert clinical significance: {}", e))?; + let result = match clinical_significance { + Benign => query.clinvar_include_benign, + LikelyBenign => query.clinvar_include_likely_benign, + UncertainSignificance => query.clinvar_include_uncertain_significance, + LikelyPathogenic => query.clinvar_include_likely_pathogenic, + Pathogenic => query.clinvar_include_pathogenic, + }; + if !result { + tracing::trace!( + "variant {:?} fails clinvar filter from query {:?}", + seqvar, + query + ); + } + Ok(result) + } else { + unreachable!("no reference clinvar assertion") + } + } else { + // Because of the annonars API, we currently need to swallow any error, + // as "not found" currently maps to an error. + Ok(true) + } +} diff --git a/src/seqvars/query/interpreter/consequences.rs b/src/seqvars/query/interpreter/consequences.rs new file mode 100644 index 00000000..2803312f --- /dev/null +++ b/src/seqvars/query/interpreter/consequences.rs @@ -0,0 +1,75 @@ +use crate::seqvars::query::schema::{CaseQuery, SequenceVariant}; + +/// Determine whether the `SequenceVariant` passes the consequences filter. +pub fn passes(query: &CaseQuery, seqvar: &SequenceVariant) -> Result { + // If no consequences are specified, the variant passes. + if query.consequences.is_empty() { + return Ok(true); + } + // Variants on chrMT always pass. + let chrom = annonars::common::cli::canonicalize(&seqvar.chrom); + if chrom == "MT" { + return Ok(true); + } + + let query_csq = std::collections::BTreeSet::from_iter(query.consequences.iter().cloned()); + for ann_field in &seqvar.ann_fields { + let seqvar_csq = + std::collections::BTreeSet::from_iter(ann_field.consequences.iter().cloned()); + let intersection_csq = query_csq.intersection(&seqvar_csq); + if intersection_csq.count() > 0 { + return Ok(true); + } + } + + tracing::trace!( + "variant {:?} fails consequence filter {:?}", + &seqvar, + &query.consequences + ); + Ok(false) +} + +#[cfg(test)] +mod test { + use mehari::annotate::seqvars::ann::{AnnField, Consequence}; + use rstest::rstest; + use strum::IntoEnumIterator; + + use crate::seqvars::query::schema::{CaseQuery, SequenceVariant}; + + #[rstest] + #[case(true)] + #[case(false)] + fn passes_consequence(#[case] c_equals_csq: bool) -> Result<(), anyhow::Error> { + for csq in Consequence::iter() { + let query = CaseQuery { + consequences: Consequence::iter() + .filter(|c| (*c == csq) == c_equals_csq) + .collect(), + ..Default::default() + }; + let seq_var = SequenceVariant { + reference: "G".into(), + alternative: "A".into(), + ann_fields: vec![AnnField { + allele: mehari::annotate::seqvars::ann::Allele::Alt { + alternative: "A".into(), + }, + consequences: vec![csq], + ..Default::default() + }], + ..Default::default() + }; + + assert_eq!( + super::passes(&query, &seq_var)?, + c_equals_csq, + "csq = {:?}", + &csq + ); + } + + Ok(()) + } +} diff --git a/src/seqvars/query/interpreter/frequency.rs b/src/seqvars/query/interpreter/frequency.rs new file mode 100644 index 00000000..fe02b4e4 --- /dev/null +++ b/src/seqvars/query/interpreter/frequency.rs @@ -0,0 +1,469 @@ +use crate::seqvars::query::schema::{CaseQuery, SequenceVariant}; + +/// Determine whether the `SequenceVariant` passes the frequency filter. +pub fn passes(query: &CaseQuery, s: &SequenceVariant) -> Result { + let q = &query; + let is_mtdna = annonars::common::cli::canonicalize(&s.chrom) == "MT"; + + if is_mtdna { + if q.helixmtdb_enabled + && (q.helixmtdb_frequency.is_some() + && s.helixmtdb_af() > q.helixmtdb_frequency.expect("tested before") + || q.helixmtdb_heteroplasmic.is_some() + && s.helix_het > q.helixmtdb_heteroplasmic.expect("tested before") + || q.helixmtdb_homoplasmic.is_some() + && s.helix_hom > q.helixmtdb_homoplasmic.expect("tested before")) + { + tracing::trace!("variant {:?} fails HelixMtDb frequency filter {:?}", s, &q); + return Ok(false); + } + } else if q.gnomad_exomes_enabled + && (q.gnomad_exomes_frequency.is_some() + && s.gnomad_exomes_af() > q.gnomad_exomes_frequency.expect("tested before") + || q.gnomad_exomes_heterozygous.is_some() + && s.gnomad_exomes_het > q.gnomad_exomes_heterozygous.expect("tested before") + || q.gnomad_exomes_homozygous.is_some() + && s.gnomad_exomes_hom > q.gnomad_exomes_homozygous.expect("tested before") + || q.gnomad_exomes_hemizygous.is_some() + && s.gnomad_exomes_hemi > q.gnomad_exomes_hemizygous.expect("tested before")) + { + tracing::trace!( + "variant {:?} fails gnomAD exomes frequency filter {:?}", + s, + &q.gnomad_exomes_frequency + ); + return Ok(false); + } + + if q.gnomad_genomes_enabled + && (q.gnomad_genomes_frequency.is_some() + && s.gnomad_genomes_af() > q.gnomad_genomes_frequency.expect("tested before") + || q.gnomad_genomes_heterozygous.is_some() + && s.gnomad_genomes_het > q.gnomad_genomes_heterozygous.expect("tested before") + || q.gnomad_genomes_homozygous.is_some() + && s.gnomad_genomes_hom > q.gnomad_genomes_homozygous.expect("tested before") + || !is_mtdna + && q.gnomad_genomes_hemizygous.is_some() + && s.gnomad_genomes_hemi > q.gnomad_genomes_hemizygous.expect("tested before")) + { + tracing::trace!( + "variant {:?} fails gnomAD genomes frequency filter {:?}", + s, + &q.gnomad_genomes_frequency + ); + return Ok(false); + } + + Ok(true) +} + +#[cfg(test)] +mod test { + use mehari::annotate::seqvars::ann::{AnnField, Consequence}; + use rstest::rstest; + + use crate::seqvars::query::schema::{CaseQuery, SequenceVariant}; + + #[rstest] + // -- frequency --------------------------------------------------------- + // frequency: pass [het count] (no filter value) + #[case(1000, 1, 0, 0, true, None, None, None, None, true)] + // frequency: pass [het count] + #[case(1000, 1, 0, 0, true, Some(0.001), None, None, None, true)] + // frequency: fail [het count] + #[case(1000, 2, 0, 0, true, Some(0.001), None, None, None, false)] + // frequency: pass [het count] (fail but filter is disabled) + #[case(1000, 2, 0, 0, false, Some(0.001), None, None, None, true)] + // frequency: pass [hom count] (no filter value) + #[case(1000, 0, 1, 0, true, None, None, None, None, true)] + // frequency: pass [hom count] + #[case(1000, 0, 1, 0, true, Some(0.002), None, None, None, true)] + // frequency: fail [hom count] + #[case(1000, 0, 2, 0, true, Some(0.002), None, None, None, false)] + // frequency: pass [hom count] (fail but filter is disabled) + #[case(1000, 0, 2, 0, false, Some(0.002), None, None, None, true)] + // frequency: pass [hemi count] (no filter value) + #[case(1000, 0, 0, 1, true, None, None, None, None, true)] + // frequency: pass [hemi count] + #[case(1000, 0, 0, 1, true, Some(0.001), None, None, None, true)] + // frequency: fail [hemi count] + #[case(1000, 0, 0, 2, true, Some(0.001), None, None, None, false)] + // frequency: pass [hemi count] (fail but filter is disabled) + #[case(1000, 0, 0, 2, false, Some(0.001), None, None, None, true)] + // -- heterezygous count ------------------------------------------------ + // het. count: pass (no filter value) + #[case(1000, 1, 0, 0, true, None, None, None, None, true)] + // het. count: pass + #[case(1000, 1, 0, 0, true, None, Some(1), None, None, true)] + // het. count: fail + #[case(1000, 2, 0, 0, true, None, Some(1), None, None, false)] + // het. count: pass (fail but filter is disabled) + #[case(1000, 2, 0, 0, false, None, Some(1), None, None, true)] + // -- homozygous count -------------------------------------------------- + // hom. count: pass (no filter value) + #[case(1000, 0, 1, 0, true, None, None, None, None, true)] + // hom. count: pass + #[case(1000, 0, 1, 0, true, None, None, Some(1), None, true)] + // hom. count: fail + #[case(1000, 0, 2, 0, true, None, None, Some(1), None, false)] + // hom. count: pass (fail but filter is disabled) + #[case(1000, 0, 2, 0, false, None, None, Some(1), None, true)] + // -- hemizygous count -------------------------------------------------- + // hemi. count: pass (no filter value) + #[case(1000, 0, 1, 0, true, None, None, None, None, true)] + // hemi. count: pass + #[case(1000, 0, 0, 1, true, None, None, None, Some(1), true)] + // hemi. count: fail + #[case(1000, 0, 0, 2, true, None, None, None, Some(1), false)] + // hemi. count: pass (fail but filter is disabled) + #[case(1000, 0, 0, 2, false, None, None, None, Some(1), true)] + fn passes_frequency_gnomad_exomes_nuclear_dna( + #[case] seqvar_gnomad_exomes_an: i32, + #[case] seqvar_gnomad_exomes_het: i32, + #[case] seqvar_gnomad_exomes_hom: i32, + #[case] seqvar_gnomad_exomes_hemi: i32, + #[case] query_gnomad_exomes_enabled: bool, + #[case] query_gnomad_exomes_frequency: Option, + #[case] query_gnomad_exomes_heterozygous: Option, + #[case] query_gnomad_exomes_homozygous: Option, + #[case] query_gnomad_exomes_hemizygous: Option, + #[case] expected_pass_all: bool, + ) -> Result<(), anyhow::Error> { + let query = CaseQuery { + gnomad_exomes_enabled: query_gnomad_exomes_enabled, + gnomad_exomes_frequency: query_gnomad_exomes_frequency, + gnomad_exomes_heterozygous: query_gnomad_exomes_heterozygous, + gnomad_exomes_homozygous: query_gnomad_exomes_homozygous, + gnomad_exomes_hemizygous: query_gnomad_exomes_hemizygous, + ..Default::default() + }; + let seq_var = SequenceVariant { + gnomad_exomes_an: seqvar_gnomad_exomes_an, + gnomad_exomes_het: seqvar_gnomad_exomes_het, + gnomad_exomes_hom: seqvar_gnomad_exomes_hom, + gnomad_exomes_hemi: seqvar_gnomad_exomes_hemi, + chrom: "X".to_string(), + reference: "G".into(), + alternative: "A".into(), + ann_fields: vec![AnnField { + allele: mehari::annotate::seqvars::ann::Allele::Alt { + alternative: "A".into(), + }, + consequences: vec![Consequence::MissenseVariant], + putative_impact: Consequence::MissenseVariant.impact(), + gene_symbol: Default::default(), + gene_id: Default::default(), + feature_type: mehari::annotate::seqvars::ann::FeatureType::SoTerm { + term: mehari::annotate::seqvars::ann::SoFeature::Transcript, + }, + feature_id: Default::default(), + feature_biotype: mehari::annotate::seqvars::ann::FeatureBiotype::Coding, + rank: Default::default(), + hgvs_t: Default::default(), + hgvs_p: Default::default(), + tx_pos: Default::default(), + cds_pos: Default::default(), + protein_pos: Default::default(), + distance: Default::default(), + messages: Default::default(), + }], + ..Default::default() + }; + + assert_eq!(super::passes(&query, &seq_var)?, expected_pass_all); + + Ok(()) + } + + #[rstest] + // -- frequency --------------------------------------------------------- + // frequency: pass [het count] (no filter value) + #[case(1000, 1, 0, 0, true, None, None, None, None, true)] + // frequency: pass [het count] + #[case(1000, 1, 0, 0, true, Some(0.001), None, None, None, true)] + // frequency: fail [het count] + #[case(1000, 2, 0, 0, true, Some(0.001), None, None, None, false)] + // frequency: pass [het count] (fail but filter is disabled) + #[case(1000, 2, 0, 0, false, Some(0.001), None, None, None, true)] + // frequency: pass [hom count] (no filter value) + #[case(1000, 0, 1, 0, true, None, None, None, None, true)] + // frequency: pass [hom count] + #[case(1000, 0, 1, 0, true, Some(0.002), None, None, None, true)] + // frequency: fail [hom count] + #[case(1000, 0, 2, 0, true, Some(0.002), None, None, None, false)] + // frequency: pass [hom count] (fail but filter is disabled) + #[case(1000, 0, 2, 0, false, Some(0.002), None, None, None, true)] + // frequency: pass [hemi count] (no filter value) + #[case(1000, 0, 0, 1, true, None, None, None, None, true)] + // frequency: pass [hemi count] + #[case(1000, 0, 0, 1, true, Some(0.001), None, None, None, true)] + // frequency: fail [hemi count] + #[case(1000, 0, 0, 2, true, Some(0.001), None, None, None, false)] + // frequency: pass [hemi count] (fail but filter is disabled) + #[case(1000, 0, 0, 2, false, Some(0.001), None, None, None, true)] + // -- heterezygous count ------------------------------------------------ + // het. count: pass (no filter value) + #[case(1000, 1, 0, 0, true, None, None, None, None, true)] + // het. count: pass + #[case(1000, 1, 0, 0, true, None, Some(1), None, None, true)] + // het. count: fail + #[case(1000, 2, 0, 0, true, None, Some(1), None, None, false)] + // het. count: pass (fail but filter is disabled) + #[case(1000, 2, 0, 0, false, None, Some(1), None, None, true)] + // -- homozygous count -------------------------------------------------- + // hom. count: pass (no filter value) + #[case(1000, 0, 1, 0, true, None, None, None, None, true)] + // hom. count: pass + #[case(1000, 0, 1, 0, true, None, None, Some(1), None, true)] + // hom. count: fail + #[case(1000, 0, 2, 0, true, None, None, Some(1), None, false)] + // hom. count: pass (fail but filter is disabled) + #[case(1000, 0, 2, 0, false, None, None, Some(1), None, true)] + // -- hemizygous count -------------------------------------------------- + // hemi. count: pass (no filter value) + #[case(1000, 0, 1, 0, true, None, None, None, None, true)] + // hemi. count: pass + #[case(1000, 0, 0, 1, true, None, None, None, Some(1), true)] + // hemi. count: fail + #[case(1000, 0, 0, 2, true, None, None, None, Some(1), false)] + // hemi. count: pass (fail but filter is disabled) + #[case(1000, 0, 0, 2, false, None, None, None, Some(1), true)] + fn passes_frequency_gnomad_genomes_nuclear_dna( + #[case] seqvar_gnomad_genomes_an: i32, + #[case] seqvar_gnomad_genomes_het: i32, + #[case] seqvar_gnomad_genomes_hom: i32, + #[case] seqvar_gnomad_genomes_hemi: i32, + #[case] query_gnomad_genomes_enabled: bool, + #[case] query_gnomad_genomes_frequency: Option, + #[case] query_gnomad_genomes_heterozygous: Option, + #[case] query_gnomad_genomes_homozygous: Option, + #[case] query_gnomad_genomes_hemizygous: Option, + #[case] expected_pass_all: bool, + ) -> Result<(), anyhow::Error> { + let query = CaseQuery { + gnomad_genomes_enabled: query_gnomad_genomes_enabled, + gnomad_genomes_frequency: query_gnomad_genomes_frequency, + gnomad_genomes_heterozygous: query_gnomad_genomes_heterozygous, + gnomad_genomes_homozygous: query_gnomad_genomes_homozygous, + gnomad_genomes_hemizygous: query_gnomad_genomes_hemizygous, + ..Default::default() + }; + let seq_var = SequenceVariant { + gnomad_genomes_an: seqvar_gnomad_genomes_an, + gnomad_genomes_het: seqvar_gnomad_genomes_het, + gnomad_genomes_hom: seqvar_gnomad_genomes_hom, + gnomad_genomes_hemi: seqvar_gnomad_genomes_hemi, + chrom: "X".to_string(), + reference: "G".into(), + alternative: "A".into(), + ann_fields: vec![AnnField { + allele: mehari::annotate::seqvars::ann::Allele::Alt { + alternative: "A".into(), + }, + consequences: vec![Consequence::MissenseVariant], + putative_impact: Consequence::MissenseVariant.impact(), + gene_symbol: Default::default(), + gene_id: Default::default(), + feature_type: mehari::annotate::seqvars::ann::FeatureType::SoTerm { + term: mehari::annotate::seqvars::ann::SoFeature::Transcript, + }, + feature_id: Default::default(), + feature_biotype: mehari::annotate::seqvars::ann::FeatureBiotype::Coding, + rank: Default::default(), + hgvs_t: Default::default(), + hgvs_p: Default::default(), + tx_pos: Default::default(), + cds_pos: Default::default(), + protein_pos: Default::default(), + distance: Default::default(), + messages: Default::default(), + }], + ..Default::default() + }; + + assert_eq!(super::passes(&query, &seq_var)?, expected_pass_all); + + Ok(()) + } + + #[rstest] + // -- frequency --------------------------------------------------------- + // frequency: pass [het count] (no filter value) + #[case(1000, 1, 0, true, None, None, None, true)] + // frequency: pass [het count] + #[case(1000, 1, 0, true, Some(0.001), None, None, true)] + // frequency: fail [het count] + #[case(1000, 2, 0, true, Some(0.001), None, None, false)] + // frequency: pass [het count] (fail but filter is disabled) + #[case(1000, 2, 0, false, Some(0.001), None, None, true)] + // frequency: pass [hom count] (no filter value) + #[case(1000, 0, 1, true, None, None, None, true)] + // frequency: pass [hom count] + #[case(1000, 0, 1, true, Some(0.002), None, None, true)] + // frequency: fail [hom count] + #[case(1000, 0, 2, true, Some(0.002), None, None, false)] + // frequency: pass [hom count] (fail but filter is disabled) + #[case(1000, 0, 2, false, Some(0.002), None, None, true)] + // -- heteroplasmy count ------------------------------------------------ + // het. count: pass (no filter value) + #[case(1000, 1, 0, true, None, None, None, true)] + // het. count: pass + #[case(1000, 1, 0, true, None, Some(1), None, true)] + // het. count: fail + #[case(1000, 2, 0, true, None, Some(1), None, false)] + // het. count: pass (fail but filter is disabled) + #[case(1000, 2, 0, false, None, Some(1), None, true)] + // -- homoplasmy count -------------------------------------------------- + // hom. count: pass (no filter value) + #[case(1000, 0, 1, true, None, None, None, true)] + // hom. count: pass + #[case(1000, 0, 1, true, None, None, Some(1), true)] + // hom. count: fail + #[case(1000, 0, 2, true, None, None, Some(1), false)] + // hom. count: pass (fail but filter is disabled) + #[case(1000, 0, 2, false, None, None, Some(1), true)] + fn passes_frequency_helix_chrmt( + #[case] seqvar_helix_an: i32, + #[case] seqvar_helix_het: i32, + #[case] seqvar_helix_hom: i32, + #[case] query_helix_enabled: bool, + #[case] query_helix_frequency: Option, + #[case] query_helix_heteroplasmic: Option, + #[case] query_helix_homoplasmic: Option, + #[case] expected_pass_all: bool, + ) -> Result<(), anyhow::Error> { + let query = CaseQuery { + helixmtdb_enabled: query_helix_enabled, + helixmtdb_frequency: query_helix_frequency, + helixmtdb_heteroplasmic: query_helix_heteroplasmic, + helixmtdb_homoplasmic: query_helix_homoplasmic, + ..Default::default() + }; + let seq_var = SequenceVariant { + helix_an: seqvar_helix_an, + helix_het: seqvar_helix_het, + helix_hom: seqvar_helix_hom, + chrom: "MT".to_string(), + reference: "G".into(), + alternative: "A".into(), + ann_fields: vec![AnnField { + allele: mehari::annotate::seqvars::ann::Allele::Alt { + alternative: "A".into(), + }, + consequences: vec![Consequence::MissenseVariant], + putative_impact: Consequence::MissenseVariant.impact(), + gene_symbol: Default::default(), + gene_id: Default::default(), + feature_type: mehari::annotate::seqvars::ann::FeatureType::SoTerm { + term: mehari::annotate::seqvars::ann::SoFeature::Transcript, + }, + feature_id: Default::default(), + feature_biotype: mehari::annotate::seqvars::ann::FeatureBiotype::Coding, + rank: Default::default(), + hgvs_t: Default::default(), + hgvs_p: Default::default(), + tx_pos: Default::default(), + cds_pos: Default::default(), + protein_pos: Default::default(), + distance: Default::default(), + messages: Default::default(), + }], + ..Default::default() + }; + + assert_eq!(super::passes(&query, &seq_var)?, expected_pass_all); + + Ok(()) + } + + #[rstest] + // -- frequency --------------------------------------------------------- + // frequency: pass [het count] (no filter value) + #[case(1000, 1, 0, true, None, None, None, true)] + // frequency: pass [het count] + #[case(1000, 1, 0, true, Some(0.001), None, None, true)] + // frequency: fail [het count] + #[case(1000, 2, 0, true, Some(0.001), None, None, false)] + // frequency: pass [het count] (fail but filter is disabled) + #[case(1000, 2, 0, false, Some(0.001), None, None, true)] + // frequency: pass [hom count] (no filter value) + #[case(1000, 0, 1, true, None, None, None, true)] + // frequency: pass [hom count] + #[case(1000, 0, 1, true, Some(0.002), None, None, true)] + // frequency: fail [hom count] + #[case(1000, 0, 2, true, Some(0.002), None, None, false)] + // frequency: pass [hom count] (fail but filter is disabled) + #[case(1000, 0, 2, false, Some(0.002), None, None, true)] + // -- heteroplasmy count ------------------------------------------------ + // het. count: pass (no filter value) + #[case(1000, 1, 0, true, None, None, None, true)] + // het. count: pass + #[case(1000, 1, 0, true, None, Some(1), None, true)] + // het. count: fail + #[case(1000, 2, 0, true, None, Some(1), None, false)] + // het. count: pass (fail but filter is disabled) + #[case(1000, 2, 0, false, None, Some(1), None, true)] + // -- homoplasmy count -------------------------------------------------- + // hom. count: pass (no filter value) + #[case(1000, 0, 1, true, None, None, None, true)] + // hom. count: pass + #[case(1000, 0, 1, true, None, None, Some(1), true)] + // hom. count: fail + #[case(1000, 0, 2, true, None, None, Some(1), false)] + // hom. count: pass (fail but filter is disabled) + #[case(1000, 0, 2, false, None, None, Some(1), true)] + #[allow(clippy::too_many_arguments)] + fn passes_frequency_gnomad_genomes_chrmt( + #[case] seqvar_gnomad_genomes_an: i32, + #[case] seqvar_gnomad_genomes_het: i32, + #[case] seqvar_gnomad_genomes_hom: i32, + #[case] query_gnomad_genomes_enabled: bool, + #[case] query_gnomad_genomes_frequency: Option, + #[case] query_gnomad_genomes_heteroplasmic: Option, + #[case] query_gnomad_genomes_homoplasmic: Option, + #[case] expected_pass_all: bool, + ) -> Result<(), anyhow::Error> { + let query = CaseQuery { + gnomad_genomes_enabled: query_gnomad_genomes_enabled, + gnomad_genomes_frequency: query_gnomad_genomes_frequency, + gnomad_genomes_heterozygous: query_gnomad_genomes_heteroplasmic, + gnomad_genomes_homozygous: query_gnomad_genomes_homoplasmic, + ..Default::default() + }; + let seq_var = SequenceVariant { + gnomad_genomes_an: seqvar_gnomad_genomes_an, + gnomad_genomes_het: seqvar_gnomad_genomes_het, + gnomad_genomes_hom: seqvar_gnomad_genomes_hom, + chrom: "MT".to_string(), + reference: "G".into(), + alternative: "A".into(), + ann_fields: vec![AnnField { + allele: mehari::annotate::seqvars::ann::Allele::Alt { + alternative: "A".into(), + }, + consequences: vec![Consequence::MissenseVariant], + putative_impact: Consequence::MissenseVariant.impact(), + gene_symbol: Default::default(), + gene_id: Default::default(), + feature_type: mehari::annotate::seqvars::ann::FeatureType::SoTerm { + term: mehari::annotate::seqvars::ann::SoFeature::Transcript, + }, + feature_id: Default::default(), + feature_biotype: mehari::annotate::seqvars::ann::FeatureBiotype::Coding, + rank: Default::default(), + hgvs_t: Default::default(), + hgvs_p: Default::default(), + tx_pos: Default::default(), + cds_pos: Default::default(), + protein_pos: Default::default(), + distance: Default::default(), + messages: Default::default(), + }], + ..Default::default() + }; + + assert_eq!(super::passes(&query, &seq_var)?, expected_pass_all); + + Ok(()) + } +} diff --git a/src/seqvars/query/interpreter/genes_allowlist.rs b/src/seqvars/query/interpreter/genes_allowlist.rs new file mode 100644 index 00000000..1708aa3a --- /dev/null +++ b/src/seqvars/query/interpreter/genes_allowlist.rs @@ -0,0 +1,94 @@ +use std::collections::HashSet; + +use crate::seqvars::query::schema::SequenceVariant; + +/// Determine whether the `SequenceVariant` passes the genes allowlist filter. +pub fn passes(hgnc_allowlist: &Option>, seqvar: &SequenceVariant) -> bool { + if let Some(hgnc_allowlist) = &hgnc_allowlist { + if hgnc_allowlist.is_empty() { + true + } else { + let res = seqvar + .ann_fields + .iter() + .any(|ann_field| hgnc_allowlist.contains(&ann_field.gene_id)); + if !res { + tracing::trace!( + "variant {:?} fails gene allowlist filter {:?}", + seqvar, + &hgnc_allowlist + ); + } + res + } + } else { + true + } +} + +#[cfg(test)] +mod test { + use rstest::rstest; + + use crate::seqvars::query::schema::SequenceVariant; + use mehari::annotate::seqvars::ann::AnnField; + + #[rstest] + #[case(None, None, true)] + #[case( + Some(vec![]), + None, + true, + )] + #[case( + Some(vec![String::from("HGNC:1100")]), + None, + false, + )] + #[case( + Some(vec![String::from("HGNC:1")]), + Some(String::from("HGNC:1100")), + false, + )] + #[case( + Some(vec![String::from("HGNC:1100")]), + Some(String::from("HGNC:1100")), + true, + )] + #[case( + Some(vec![String::from("HGNC:1"), String::from("HGNC:1100")]), + Some(String::from("HGNC:1100")), + true, + )] + fn passes( + #[case] hgnc_allowlist: Option>, + #[case] seqvar_gene: Option, + #[case] expected: bool, + ) { + let hgnc_allowlist = hgnc_allowlist.map(|hgnc_allowlist| { + hgnc_allowlist + .into_iter() + .map(|hgnc_id| hgnc_id.to_uppercase()) + .collect::>() + }); + let seqvar = SequenceVariant { + ann_fields: if let Some(gene_id) = seqvar_gene.as_ref() { + vec![AnnField { + gene_id: gene_id.clone(), + ..Default::default() + }] + } else { + vec![] + }, + ..Default::default() + }; + + assert_eq!( + super::passes(&hgnc_allowlist, &seqvar), + expected, + "hgnc_allowlist: {:?}, seqvar_genes: {:?}", + hgnc_allowlist, + seqvar_gene + ) + } +} diff --git a/src/seqvars/query/interpreter/genotype.rs b/src/seqvars/query/interpreter/genotype.rs new file mode 100644 index 00000000..24298769 --- /dev/null +++ b/src/seqvars/query/interpreter/genotype.rs @@ -0,0 +1,647 @@ +use crate::seqvars::query::schema::{CaseQuery, GenotypeChoice, SequenceVariant}; + +/// Determine whether the `SequenceVariant` passes the genotype filter. +pub fn passes( + query: &CaseQuery, + seqvar: &SequenceVariant, + no_call_samples: &[&str], +) -> Result { + let result = if query.recessive_mode() { + let index_sample = query.index_sample().ok_or_else(|| { + anyhow::anyhow!("recessive mode requires an index sample, but none was found") + })?; + passes_recessive_modes(&query.genotype, &index_sample, seqvar, no_call_samples)? + } else { + passes_non_recessive_mode(&query.genotype, seqvar, no_call_samples)? + }; + + if !result { + tracing::trace!( + "variant {:?} fails for genotype filter {:?}", + seqvar, + &query.genotype + ); + } + Ok(result) +} + +/// Handle case of the mode being one of the recessive modes. +fn passes_recessive_modes( + query_genotype: &indexmap::IndexMap>, + index_name: &str, + seqvar: &SequenceVariant, + no_call_samples: &[&str], +) -> Result { + // Get genotype choice of index. + let index_gt_choice = query_genotype + .get(index_name) + .ok_or_else(|| { + anyhow::anyhow!( + "index sample {} not found in genotype filter {:?}", + &index_name, + &query_genotype + ) + })? + .ok_or_else(|| { + anyhow::anyhow!( + "index sample {} has no genotype choice in genotype filter {:?}", + &index_name, + &query_genotype + ) + })?; + // For recessive mode, we have to know the samples selected for index and parents. + let index_gt_string = if no_call_samples.contains(&index_name) { + String::from(".") + } else { + let call_info = seqvar.call_info.get(index_name).ok_or_else(|| { + anyhow::anyhow!( + "index sample {} not found in call info for {:?}", + &index_name, + &seqvar + ) + })?; + call_info.genotype.as_ref().cloned().ok_or_else(|| { + anyhow::anyhow!( + "index sample {} has no genotype in call info for {:?}", + &index_name, + &seqvar + ) + })? + }; + let parent_names = query_genotype + .iter() + .flat_map(|(sample, choice)| { + if matches!( + choice, + Some(crate::seqvars::query::schema::GenotypeChoice::RecessiveParent) + ) { + Some(sample.clone()) + } else { + None + } + }) + .collect::>(); + let parent_gt_strings = parent_names + .iter() + .map(|parent_name| { + if no_call_samples.contains(&parent_name.as_str()) { + Ok(String::from(".")) // no-call + } else { + seqvar + .call_info + .get(parent_name) + .cloned() + .ok_or_else(|| { + anyhow::anyhow!( + "parent sample {} not found in call info for {:?}", + &parent_name, + &seqvar + ) + })? + .genotype + .ok_or_else(|| { + anyhow::anyhow!( + "parent sample {} has no genotype in call info for {:?}", + &parent_name, + &seqvar + ) + }) + } + }) + .collect::, _>>()?; + + let compound_recessive_ok_index = crate::seqvars::query::schema::GenotypeChoice::Het + .matches(&index_gt_string) + .map_err(|e| anyhow::anyhow!("invalid index genotype: {}", e))?; + let compound_recessive_parents_ref = parent_gt_strings + .iter() + .filter(|parent_gt_string| { + crate::seqvars::query::schema::GenotypeChoice::Ref + .matches(parent_gt_string) + .unwrap_or(false) + }) + .count(); + let compound_recessive_parents_het = parent_gt_strings + .iter() + .filter(|parent_gt_string| { + crate::seqvars::query::schema::GenotypeChoice::Het + .matches(parent_gt_string) + .unwrap_or(false) + }) + .count(); + let compound_recessive_parents_hom = parent_gt_strings + .iter() + .filter(|parent_gt_string| { + crate::seqvars::query::schema::GenotypeChoice::Hom + .matches(parent_gt_string) + .unwrap_or(false) + }) + .count(); + + let compound_recessive_ok = match parent_names.len() { + 0 => compound_recessive_ok_index, + 1 => { + compound_recessive_ok_index + && compound_recessive_parents_ref + compound_recessive_parents_het == 1 + && compound_recessive_parents_hom == 0 + } + 2 => { + compound_recessive_ok_index + && compound_recessive_parents_ref == 1 + && compound_recessive_parents_het == 1 + && compound_recessive_parents_hom == 0 + } + _ => anyhow::bail!("more than two recessive parents selected"), + }; + + let homozygous_recessive_ok_index = crate::seqvars::query::schema::GenotypeChoice::Hom + .matches(&index_gt_string) + .map_err(|e| anyhow::anyhow!("invalid index genotype: {}", e))?; + let homozygous_recessive_ok_parents = parent_gt_strings + .iter() + .map(|parent_gt_string| { + crate::seqvars::query::schema::GenotypeChoice::Het + .matches(parent_gt_string) + .map_err(|e| anyhow::anyhow!("invalid parent genotype: {}", e)) + }) + .collect::, _>>()?; + let homozygous_recessive_ok = + homozygous_recessive_ok_index && homozygous_recessive_ok_parents.iter().all(|&ok| ok); + + match index_gt_choice { + GenotypeChoice::ComphetIndex => Ok(compound_recessive_ok), + GenotypeChoice::RecessiveIndex => Ok(compound_recessive_ok || homozygous_recessive_ok), + _ => anyhow::bail!( + "invalid genotype choice for recessive mode: {:?}", + index_gt_choice + ), + } +} + +/// Handle case if the mode is not "recessive". Note that this actually includes the +/// homozygous recessive mode. +fn passes_non_recessive_mode( + query_genotype: &indexmap::IndexMap>, + seqvar: &SequenceVariant, + no_call_samples: &[&str], +) -> Result { + for (sample_name, genotype) in query_genotype.iter() { + let genotype_choice = if let Some(genotype_choice) = genotype { + genotype_choice + } else { + tracing::trace!("no genotype choice for sample {} (skip&pass)", sample_name); + continue; + }; + let genotype = if no_call_samples.contains(&sample_name.as_str()) { + "." // no-call + } else if let Some(call_info) = seqvar.call_info.get(sample_name) { + if let Some(genotype) = call_info.genotype.as_ref() { + genotype + } else { + tracing::trace!("no GT for sample {} (skip&fail)", sample_name); + return Ok(false); + } + } else { + tracing::trace!("no call info for sample {} (skip&fail)", sample_name); + return Ok(false); + }; + + if !genotype_choice + .matches(genotype) + .map_err(|e| anyhow::anyhow!("invalid genotype choice in {:?}: {}", &seqvar, e))? + { + tracing::trace!( + "variant {:?} fails genotype filter {:?} on sample {}", + seqvar, + &query_genotype, + sample_name + ); + return Ok(false); + } + } + + Ok(true) // all good up to here +} + +#[cfg(test)] +mod test { + use rstest::rstest; + + use crate::seqvars::query::schema::{ + CallInfo, + GenotypeChoice::{self, *}, + SequenceVariant, + }; + + static INDEX_NAME: &str = "sample"; + static FATHER_NAME: &str = "father"; + static MOTHER_NAME: &str = "mother"; + + #[rstest] + // any: passes + #[case("0/0", Any, true)] + #[case("0|0", Any, true)] + #[case("0/1", Any, true)] + #[case("0|1", Any, true)] + #[case("0", Any, true)] + #[case("1/0", Any, true)] + #[case("1|0", Any, true)] + #[case("1/1", Any, true)] + #[case("1|1", Any, true)] + #[case("1", Any, true)] + #[case(".", Any, true)] + #[case("./.", Any, true)] + #[case(".|.", Any, true)] + // ref: passes + #[case("0/0", Ref, true)] + #[case("0|0", Ref, true)] + #[case("0", Ref, true)] + // ref: passes NOT + #[case("0/1", Ref, false)] + #[case("0|1", Ref, false)] + #[case("1/0", Ref, false)] + #[case("1|0", Ref, false)] + #[case("1/1", Ref, false)] + #[case("1|1", Ref, false)] + #[case("1", Ref, false)] + #[case(".", Ref, false)] + #[case("./.", Ref, false)] + #[case(".|.", Ref, false)] + // het: passes + #[case("0/1", Het, true)] + #[case("0|1", Het, true)] + #[case("1/0", Het, true)] + #[case("1|0", Het, true)] + // het: passes NOT + #[case("0/0", Het, false)] + #[case("0|0", Het, false)] + #[case("0", Het, false)] + #[case("1/1", Het, false)] + #[case("1|1", Het, false)] + #[case("1", Het, false)] + #[case(".", Het, false)] + #[case("./.", Het, false)] + #[case(".|.", Het, false)] + // hom: passes + #[case("1/1", Hom, true)] + #[case("1|1", Hom, true)] + #[case("1", Hom, true)] + // hom: passes NOT + #[case("0/0", Hom, false)] + #[case("0|0", Hom, false)] + #[case("0/1", Hom, false)] + #[case("0|1", Hom, false)] + #[case("0", Hom, false)] + #[case("1/0", Hom, false)] + #[case("1|0", Hom, false)] + #[case(".", Hom, false)] + #[case("./.", Hom, false)] + #[case(".|.", Hom, false)] + // non-hom: passes + #[case("0/0", NonHom, true)] + #[case("0|0", NonHom, true)] + #[case("0/1", NonHom, true)] + #[case("0|1", NonHom, true)] + #[case("0", NonHom, true)] + #[case("1/0", NonHom, true)] + #[case("1|0", NonHom, true)] + #[case(".", NonHom, true)] + #[case("./.", NonHom, true)] + #[case(".|.", NonHom, true)] + // non-hom: passes NOT + #[case("1/1", NonHom, false)] + #[case("1|1", NonHom, false)] + #[case("1", NonHom, false)] + // variant: passes + #[case("0/1", Variant, true)] + #[case("0|1", Variant, true)] + #[case("1/0", Variant, true)] + #[case("1|0", Variant, true)] + #[case("1/1", Variant, true)] + #[case("1|1", Variant, true)] + #[case("1", Variant, true)] + // variant: passes NOT + #[case("0/0", Variant, false)] + #[case("0|0", Variant, false)] + #[case("0", Variant, false)] + #[case(".", Variant, false)] + #[case("./.", Variant, false)] + #[case(".|.", Variant, false)] + + fn passes_non_recessive_mode_singleton( + #[case] sample_gt: &str, + #[case] query_gt: GenotypeChoice, + #[case] expected: bool, + ) -> Result<(), anyhow::Error> { + let query_genotype: indexmap::IndexMap<_, _> = + vec![(String::from(INDEX_NAME), Some(query_gt))] + .into_iter() + .collect(); + let seq_var = SequenceVariant { + call_info: vec![ + (( + INDEX_NAME.into(), + CallInfo { + genotype: Some(sample_gt.into()), + ..Default::default() + }, + )), + ] + .into_iter() + .collect(), + ..Default::default() + }; + + assert_eq!( + super::passes_non_recessive_mode(&query_genotype, &seq_var, &[])?, + expected, + "sample_gt = {}, query_gt = {:?}, expected = {}", + sample_gt, + query_gt, + expected + ); + + Ok(()) + } + + #[rstest] + // any: passes + #[case("0/0,0/0,0/0", Any, Any, Any, true)] + #[case(".,.,.", Any, Any, Any, true)] + // some combinations: passes + #[case("0/1,0/1,0/0", Het, Het, Ref, true)] + #[case("0/1,0|1,0/0", Het, Het, Ref, true)] + #[case("0|1,0/1,0/0", Het, Het, Ref, true)] + #[case("0/1,0/0,0/1", Any, Ref, Het, true)] + #[case("0|1,0/0,0|1", Any, Ref, Het, true)] + #[case("0/1,0/0,0|1", Any, Ref, Het, true)] + #[case("0|1,0/0,0/1", Any, Ref, Het, true)] + #[case("0/1,0/0,0/0", Variant, Ref, Ref, true)] + #[case("0|1,0/0,0/0", Variant, Ref, Ref, true)] + #[case("1/0,0/0,0/0", Variant, Ref, Ref, true)] + #[case("1|0,0/0,0/0", Variant, Ref, Ref, true)] + #[case("1,0,0/0", Variant, Ref, Ref, true)] + // some combinations: passes NOT + #[case("0/0,0/0,0/0", Het, Any, Any, false)] + #[case("0/0,0/0,0/0", Any, Het, Any, false)] + #[case("0/0,0/0,0/0", Any, Any, Het, false)] + #[case("1,0,0/1", Variant, Ref, Ref, false)] + #[case("1,0,.", Variant, Ref, Ref, false)] + fn passes_non_recessive_mode_trio( + #[case] sample_gts: &str, + #[case] query_gt_index: GenotypeChoice, + #[case] query_gt_father: GenotypeChoice, + #[case] query_gt_mother: GenotypeChoice, + #[case] expected: bool, + ) -> Result<(), anyhow::Error> { + let query_genotype: indexmap::IndexMap<_, _> = vec![ + (String::from(INDEX_NAME), Some(query_gt_index)), + (String::from(FATHER_NAME), Some(query_gt_father)), + (String::from(MOTHER_NAME), Some(query_gt_mother)), + ] + .into_iter() + .collect(); + let sample_gts = sample_gts + .split(',') + .map(|s| s.to_string()) + .collect::>(); + let seq_var = SequenceVariant { + call_info: vec![ + ( + String::from(INDEX_NAME), + CallInfo { + genotype: Some(sample_gts[0].clone()), + ..Default::default() + }, + ), + ( + String::from(FATHER_NAME), + CallInfo { + genotype: Some(sample_gts[1].clone()), + ..Default::default() + }, + ), + ( + String::from(MOTHER_NAME), + CallInfo { + genotype: Some(sample_gts[2].clone()), + ..Default::default() + }, + ), + ] + .into_iter() + .collect(), + ..Default::default() + }; + + assert_eq!( + super::passes_non_recessive_mode(&query_genotype, &seq_var, &[])?, + expected, + "sample_gt = {:?}, query_gt_index = {:?}, query_gt_father = {:?}, \ + query_gt_mother = {:?}, expected = {}", + sample_gts, + query_gt_index, + query_gt_father, + query_gt_mother, + expected + ); + + Ok(()) + } + + #[rstest] + // any: passes + #[case("0/0", ComphetIndex)] + #[case("0/0", RecessiveIndex)] + #[case("0/0", RecessiveParent)] + fn passes_non_recessive_mode_fails_on_recessive_markers( + #[case] sample_gt: &str, + #[case] query_gt: GenotypeChoice, + ) -> Result<(), anyhow::Error> { + let query_genotype: indexmap::IndexMap<_, _> = + vec![(String::from(INDEX_NAME), Some(query_gt))] + .into_iter() + .collect(); + let seq_var = SequenceVariant { + call_info: vec![ + (( + INDEX_NAME.into(), + CallInfo { + genotype: Some(sample_gt.into()), + ..Default::default() + }, + )), + ] + .into_iter() + .collect(), + ..Default::default() + }; + + assert!(super::passes_non_recessive_mode(&query_genotype, &seq_var, &[]).is_err(),); + + Ok(()) + } + + #[rstest] + // comphet-index: passes + #[case("0/1", ComphetIndex, true)] + #[case("0|1", ComphetIndex, true)] + #[case("1/0", ComphetIndex, true)] + #[case("1|0", ComphetIndex, true)] + // comphet-index: passes NOT + #[case("0/0", ComphetIndex, false)] + #[case("0|0", ComphetIndex, false)] + #[case("0", ComphetIndex, false)] + #[case("1/1", ComphetIndex, false)] + #[case("1|1", ComphetIndex, false)] + #[case("1", ComphetIndex, false)] + #[case(".", ComphetIndex, false)] + #[case("./.", ComphetIndex, false)] + #[case(".|.", ComphetIndex, false)] + // recessive-index: passes + #[case("0/1", RecessiveIndex, true)] + #[case("0|1", RecessiveIndex, true)] + #[case("1/0", RecessiveIndex, true)] + #[case("1|0", RecessiveIndex, true)] + #[case("1/1", RecessiveIndex, true)] + #[case("1|1", RecessiveIndex, true)] + #[case("1", RecessiveIndex, true)] + // recessive-index: passes NOT + #[case("0/0", RecessiveIndex, false)] + #[case("0|0", RecessiveIndex, false)] + #[case("0", RecessiveIndex, false)] + #[case(".", RecessiveIndex, false)] + #[case("./.", RecessiveIndex, false)] + #[case(".|.", RecessiveIndex, false)] + fn passes_recessive_modes_singleton( + #[case] sample_gt: &str, + #[case] query_gt: GenotypeChoice, + #[case] expected: bool, + ) -> Result<(), anyhow::Error> { + let query_genotype: indexmap::IndexMap<_, _> = + vec![(String::from(INDEX_NAME), Some(query_gt))] + .into_iter() + .collect(); + let seq_var = SequenceVariant { + call_info: vec![ + (( + INDEX_NAME.into(), + CallInfo { + genotype: Some(sample_gt.into()), + ..Default::default() + }, + )), + ] + .into_iter() + .collect(), + ..Default::default() + }; + + assert_eq!( + super::passes_recessive_modes(&query_genotype, INDEX_NAME, &seq_var, &[])?, + expected, + "sample_gt = {}, query_gt = {:?}, expected = {}", + sample_gt, + query_gt, + expected + ); + + Ok(()) + } + + #[rstest] + // recessive mode: passes + #[case("0/1,0/0,0/0", RecessiveIndex, Any, Any, true)] + #[case("0|1,0/0,0/0", RecessiveIndex, Any, Any, true)] + #[case("1/0,0/0,0/0", RecessiveIndex, Any, Any, true)] + #[case("1|0,0/0,0/0", RecessiveIndex, Any, Any, true)] + #[case("1/0,0/1,0/0", RecessiveIndex, RecessiveParent, RecessiveParent, true)] + #[case("1/0,0/0,0/1", RecessiveIndex, RecessiveParent, RecessiveParent, true)] + #[case("1/1,0/1,0/1", RecessiveIndex, RecessiveParent, RecessiveParent, true)] + #[case("1/1,0/0,0/1", RecessiveIndex, Any, RecessiveParent, true)] + #[case("1/1,0/1,0/0", RecessiveIndex, RecessiveParent, Any, true)] + #[case("1|1,0|1,1|0", RecessiveIndex, RecessiveParent, RecessiveParent, true)] + // recessive mode: passes NOT + #[case("1/1,1/1,0/0", RecessiveIndex, RecessiveParent, Any, false)] + #[case("0/1,0/0,0/0", RecessiveIndex, RecessiveParent, RecessiveParent, false)] + #[case("0/1,1/1,0/0", RecessiveIndex, RecessiveParent, RecessiveParent, false)] + #[case("0/1,0/0,1/1", RecessiveIndex, RecessiveParent, RecessiveParent, false)] + #[case("0/1,0/1,0/1", RecessiveIndex, RecessiveParent, RecessiveParent, false)] + // compound recessive mode: passes + #[case("0/1,0/0,0/0", ComphetIndex, Any, Any, true)] + #[case("0|1,0/0,0/0", ComphetIndex, Any, Any, true)] + #[case("1/0,0/0,0/0", ComphetIndex, Any, Any, true)] + #[case("1|0,0/0,0/0", ComphetIndex, Any, Any, true)] + #[case("0/1,1/1,0/0", ComphetIndex, Any, RecessiveParent, true)] + #[case("0/1,0/0,1/1", ComphetIndex, RecessiveParent, Any, true)] + #[case("1/0,0/1,0/0", ComphetIndex, RecessiveParent, RecessiveParent, true)] + #[case("1/0,0/0,0/1", ComphetIndex, RecessiveParent, RecessiveParent, true)] + // compound recessive mode: passes NOT + #[case("1/1,0/1,0/1", ComphetIndex, RecessiveParent, RecessiveParent, false)] + #[case("1|1,0|1,1|0", ComphetIndex, RecessiveParent, RecessiveParent, false)] + #[case("0/1,0/0,0/0", ComphetIndex, RecessiveParent, RecessiveParent, false)] + #[case("0/1,1/1,0/0", ComphetIndex, RecessiveParent, RecessiveParent, false)] + #[case("0/1,0/0,1/1", ComphetIndex, RecessiveParent, RecessiveParent, false)] + #[case("0/1,0/1,0/1", ComphetIndex, RecessiveParent, RecessiveParent, false)] + fn passes_recessive_modes_trio( + #[case] sample_gts: &str, + #[case] query_gt_index: GenotypeChoice, + #[case] query_gt_father: GenotypeChoice, + #[case] query_gt_mother: GenotypeChoice, + #[case] expected: bool, + ) -> Result<(), anyhow::Error> { + let query_genotype: indexmap::IndexMap<_, _> = vec![ + (String::from(INDEX_NAME), Some(query_gt_index)), + (String::from(FATHER_NAME), Some(query_gt_father)), + (String::from(MOTHER_NAME), Some(query_gt_mother)), + ] + .into_iter() + .collect(); + let sample_gts = sample_gts + .split(',') + .map(|s| s.to_string()) + .collect::>(); + let seq_var = SequenceVariant { + call_info: vec![ + ( + String::from(INDEX_NAME), + CallInfo { + genotype: Some(sample_gts[0].clone()), + ..Default::default() + }, + ), + ( + String::from(FATHER_NAME), + CallInfo { + genotype: Some(sample_gts[1].clone()), + ..Default::default() + }, + ), + ( + String::from(MOTHER_NAME), + CallInfo { + genotype: Some(sample_gts[2].clone()), + ..Default::default() + }, + ), + ] + .into_iter() + .collect(), + ..Default::default() + }; + + assert_eq!( + super::passes_recessive_modes(&query_genotype, INDEX_NAME, &seq_var, &[])?, + expected, + "sample_gt = {:?}, query_gt_index = {:?}, query_gt_father = {:?}, \ + query_gt_mother = {:?}, expected = {}", + sample_gts, + query_gt_index, + query_gt_father, + query_gt_mother, + expected + ); + + Ok(()) + } +} diff --git a/src/seqvars/query/interpreter/mod.rs b/src/seqvars/query/interpreter/mod.rs new file mode 100644 index 00000000..e2689a04 --- /dev/null +++ b/src/seqvars/query/interpreter/mod.rs @@ -0,0 +1,81 @@ +//! Apply settings from a `strucvar::query::schema::CaseQuery` to `SequenceVariant` records. + +use std::collections::HashSet; + +mod clinvar; +mod consequences; +mod frequency; +mod genes_allowlist; +mod genotype; +mod quality; +mod regions_allowlist; + +use super::{ + annonars::Annotator, + schema::{CaseQuery, SequenceVariant}, +}; + +/// Hold data structures that support the interpretation of one `CaseQuery` +/// to multiple `StructuralVariant` records. +#[derive(Debug, Default)] +pub struct QueryInterpreter { + /// The case query settings. + pub query: CaseQuery, + /// Gene allowlist with HGNC IDs. + pub hgnc_allowlist: Option>, +} + +/// Result type for `QueryInterpreter::passes_genotype()`. +#[derive(Debug, Default)] +pub struct PassesResult { + /// Whether genotype passes for all samples. + pub pass_all: bool, +} + +impl QueryInterpreter { + /// Construct new `QueryInterpreter` with the given query settings. + pub fn new(query: CaseQuery, hgnc_allowlist: Option>) -> Self { + QueryInterpreter { + query, + hgnc_allowlist, + } + } + + /// Determine whether the annotated `SequenceVariant` passes all criteria. + pub fn passes( + &self, + seqvar: &SequenceVariant, + annotator: &Annotator, + ) -> Result { + // Check the filters first that are cheap to compute. + let pass_frequency = frequency::passes(&self.query, seqvar)?; + let pass_consequences = consequences::passes(&self.query, seqvar)?; + let res_quality = quality::passes(&self.query, seqvar)?; + let pass_genes_allowlist = genes_allowlist::passes(&self.hgnc_allowlist, seqvar); + let pass_regions_allowlist = regions_allowlist::passes(&self.query, seqvar); + if !pass_frequency + || !pass_consequences + || !res_quality.pass + || !pass_genes_allowlist + || !pass_regions_allowlist + { + return Ok(PassesResult { pass_all: false }); + } + // Now also check the genotype that needs the quality filter output as input. + if !genotype::passes( + &self.query, + seqvar, + &res_quality + .no_call_samples + .iter() + .map(|s| s.as_str()) + .collect::>(), + )? { + return Ok(PassesResult { pass_all: false }); + } + // If we passed until here, check the presence in ClinVar which needs a database lookup. + Ok(PassesResult { + pass_all: clinvar::passes(&self.query, annotator, seqvar)?, + }) + } +} diff --git a/src/seqvars/query/interpreter/quality.rs b/src/seqvars/query/interpreter/quality.rs new file mode 100644 index 00000000..1d910bdc --- /dev/null +++ b/src/seqvars/query/interpreter/quality.rs @@ -0,0 +1,501 @@ +use crate::seqvars::query::schema::{ + CallInfo, CaseQuery, FailChoice, QualitySettings, SequenceVariant, +}; + +/// Return type for the `passes` function. +#[derive(Debug)] +pub struct PassOrNoCall { + /// Whether the variant should be kept. + pub pass: bool, + /// For which samples should the genotype be interpreted as no-call. + pub no_call_samples: Vec, +} + +/// Determine whether the `SequenceVariant` passes the quality filter. +/// Will return `FailChoice::Ignore` if the variant passes. +pub fn passes(query: &CaseQuery, seqvar: &SequenceVariant) -> Result { + let mut result = PassOrNoCall { + pass: true, + no_call_samples: Vec::new(), + }; + for (sample_name, quality_settings) in &query.quality { + if let Some(call_info) = seqvar.call_info.get(sample_name) { + if let Some(fail) = passes_for_sample(quality_settings, call_info) { + match fail { + FailChoice::Ignore => { + // ignore quality failure for sample + } + FailChoice::Drop => { + tracing::trace!( + "sample {} in variant {:?} fails quality filter {:?}", + &sample_name, + &seqvar, + &quality_settings + ); + result.pass = false; + break; + } + FailChoice::NoCall => { + result.no_call_samples.push(sample_name.clone()); + } + } + } else { + // no failure, all good + } + } else { + anyhow::bail!("sample {} not found in call info", sample_name); + } + } + + tracing::trace!( + "variant {:?} has result {:?} for quality filter {:?}", + seqvar, + result, + &query.genotype + ); + Ok(result) +} + +/// Return failure code (or None for all-pass) for one sample's call info. +fn passes_for_sample( + quality_settings: &QualitySettings, + call_info: &CallInfo, +) -> Option { + #[derive(PartialEq, Eq)] + enum Genotype { + Het, + Hom, + Ref, + NoCall, + } + + let genotype = if let Some(genotype) = call_info.genotype.as_ref() { + match genotype.as_str() { + "0/1" | "1/0" | "0|1" | "1|0" => Genotype::Het, + "1/1" | "1|1" | "1" => Genotype::Hom, + "0/0" | "0|0" | "0" => Genotype::Ref, + _ => Genotype::NoCall, + } + } else { + Genotype::NoCall + }; + + // dp_het/dp_hom and ab + match genotype { + Genotype::Het => { + // dp_het + if let Some(dp_het) = quality_settings.dp_het { + if let Some(dp) = call_info.dp { + if dp < dp_het { + return Some(quality_settings.fail); + } + } + } + + // ab + if let (Some(settings_ab), Some(call_dp), Some(call_ad)) = + (quality_settings.ab, call_info.dp, call_info.ad) + { + let ab_raw = call_ad as f64 / call_dp as f64; + let ab = if ab_raw > 0.5 { 1.0 - ab_raw } else { ab_raw }; + let eps = 1e-6f64; + if ab + eps < settings_ab as f64 { + return Some(quality_settings.fail); + } + } + } + Genotype::Hom => { + if let Some(dp_hom) = quality_settings.dp_hom { + if let Some(dp) = call_info.dp { + if dp < dp_hom { + return Some(quality_settings.fail); + } + } + } + } + Genotype::Ref | Genotype::NoCall => (), + } + + // gq + if let (Some(settings_gq), Some(call_gq)) = (quality_settings.gq, call_info.quality) { + if call_gq < settings_gq as f32 { + return Some(quality_settings.fail); + } + } + + if genotype != Genotype::Ref { + // ad + if let (Some(settings_ad), Some(call_ad)) = (quality_settings.ad, call_info.ad) { + if call_ad < settings_ad { + return Some(quality_settings.fail); + } + } + + // ad_max + if let (Some(settings_ad_max), Some(call_ad)) = (quality_settings.ad_max, call_info.ad) { + if call_ad > settings_ad_max { + return Some(quality_settings.fail); + } + } + } + + None +} + +#[cfg(test)] +mod test { + use rstest::rstest; + + use crate::seqvars::query::schema::{ + CallInfo, CaseQuery, + FailChoice::{self, *}, + QualitySettings, SequenceVariant, + }; + + #[rstest] + #[case(Ignore, true, true, false)] + #[case(Ignore, false, true, false)] + #[case(Drop, true, true, false)] + #[case(Drop, false, false, false)] + #[case(NoCall, true, true, false)] + #[case(NoCall, false, true, true)] + fn passes( + #[case] q_fail: FailChoice, + #[case] should_pass: bool, + #[case] expected_pass: bool, + #[case] any_no_call_sample: bool, + ) -> Result<(), anyhow::Error> { + let query = CaseQuery { + quality: vec![( + String::from("sample"), + QualitySettings { + dp_het: None, + dp_hom: None, + gq: if should_pass { None } else { Some(40) }, + ab: None, + ad: None, + ad_max: None, + fail: q_fail, + }, + )] + .into_iter() + .collect(), + ..Default::default() + }; + let seqvar = SequenceVariant { + call_info: vec![( + String::from("sample"), + CallInfo { + quality: if should_pass { None } else { Some(30f32) }, + ..Default::default() + }, + )] + .into_iter() + .collect(), + ..Default::default() + }; + + let res = super::passes(&query, &seqvar)?; + + assert_eq!( + res.pass, expected_pass, + "query = {:#?}, seqvar = {:#?}", + &query, &seqvar + ); + let expected = if any_no_call_sample { + vec![String::from("sample")] + } else { + vec![] + }; + assert_eq!( + &res.no_call_samples, &expected, + "query = {:#?}, seqvar = {:#?}", + &query, &seqvar + ); + + Ok(()) + } + + #[rstest] + // het, pass dp + #[case( + Some(10), // q_dp_het + None, // q_dp_hom + None, // q_gq + None, // q_ab + None, // q_ad + None, // q_ad_max + Ignore, // q_fail + Some("0/1"), // c_genotype + None, // c_quality + Some(10), // c_dp + None, // c_ad + None, // expected, None = pass + )] + // het, fail dp + #[case( + Some(10), // q_dp_het + None, // q_dp_hom + None, // q_gq + None, // q_ab + None, // q_ad + None, // q_ad_max + Ignore, // q_fail + Some("0/1"), // c_genotype + None, // c_quality + Some(9), // c_dp + None, // c_ad + Some(Ignore), // expected, None = pass + )] + // hom, pass dp + #[case( + None, // q_dp_het + Some(10), // q_dp_hom + None, // q_gq + None, // q_ab + None, // q_ad + None, // q_ad_max + Ignore, // q_fail + Some("1/1"), // c_genotype + None, // c_quality + Some(10), // c_dp + None, // c_ad + None, // expected, None = pass + )] + // hom, fail dp + #[case( + None, // q_dp_het + Some(10), // q_dp_hom + None, // q_gq + None, // q_ab + None, // q_ad + None, // q_ad_max + Ignore, // q_fail + Some("1/1"), // c_genotype + None, // c_quality + Some(9), // c_dp + None, // c_ad + Some(Ignore), // expected, None = pass + )] + // pass gq + #[case( + None, // q_dp_het + None, // q_dp_hom + Some(10), // q_gq + None, // q_ab + None, // q_ad + None, // q_ad_max + Ignore, // q_fail + None, // c_genotype + Some(10f32), // c_quality + None, // c_dp + None, // c_ad + None, // expected, None = pass + )] + // fail gq + #[case( + None, // q_dp_het + None, // q_dp_hom + Some(10), // q_gq + None, // q_ab + None, // q_ad + None, // q_ad_max + Ignore, // q_fail + Some("0/1"), // c_genotype + Some(9f32), // c_quality + None, // c_dp + None, // c_ad + Some(Ignore), // expected, None = pass + )] + // het, pass ab lower + #[case( + None, // q_dp_het + None, // q_dp_hom + None, // q_gq + Some(0.2), // q_ab + None, // q_ad + None, // q_ad_max + Ignore, // q_fail + Some("0/1"), // c_genotype + None, // c_quality + Some(100), // c_dp + Some(20), // c_ad + None, // expected, None = pass + )] + // het, pass ab upper + #[case( + None, // q_dp_het + None, // q_dp_hom + None, // q_gq + Some(0.2), // q_ab + None, // q_ad + None, // q_ad_max + Ignore, // q_fail + Some("0/1"), // c_genotype + None, // c_quality + Some(100), // c_dp + Some(80), // c_ad + None, // expected, None = pass + )] + // het, fail ab lower + #[case( + None, // q_dp_het + None, // q_dp_hom + None, // q_gq + Some(0.2), // q_ab + None, // q_ad + None, // q_ad_max + Ignore, // q_fail + Some("0/1"), // c_genotype + None, // c_quality + Some(100), // c_dp + Some(19), // c_ad + Some(Ignore), // expected, None = pass + )] + // het, fail ab upper + #[case( + None, // q_dp_het + None, // q_dp_hom + None, // q_gq + Some(0.2), // q_ab + None, // q_ad + None, // q_ad_max + Ignore, // q_fail + Some("0/1"), // c_genotype + None, // c_quality + Some(100), // c_dp + Some(81), // c_ad + Some(Ignore), // expected, None = pass + )] + // hom, ab ignored + #[case( + None, // q_dp_het + None, // q_dp_hom + None, // q_gq + Some(0.2), // q_ab + None, // q_ad + None, // q_ad_max + Ignore, // q_fail + Some("1/1"), // c_genotype + None, // c_quality + None, // c_dp + None, // c_ad + None, // expected, None = pass + )] + // pass ad + #[case( + None, // q_dp_het + None, // q_dp_hom + None, // q_gq + None, // q_ab + Some(10), // q_ad + None, // q_ad_max + Ignore, // q_fail + None, // c_genotype + None, // c_quality + None, // c_dp + Some(10), // c_ad + None, // expected, None = pass + )] + // fail ad + #[case( + None, // q_dp_het + None, // q_dp_hom + None, // q_gq + None, // q_ab + Some(10), // q_ad + None, // q_ad_max + Ignore, // q_fail + None, // c_genotype + None, // c_quality + None, // c_dp + Some(9), // c_ad + Some(Ignore), // expected, None = pass + )] + // pass ad_max + #[case( + None, // q_dp_het + None, // q_dp_hom + None, // q_gq + None, // q_ab + None, // q_ad + Some(10), // q_ad_max + Ignore, // q_fail + None, // c_genotype + None, // c_quality + None, // c_dp + Some(10), // c_ad + None, // expected, None = pass + )] + // fail ad_max + #[case( + None, // q_dp_het + None, // q_dp_hom + None, // q_gq + None, // q_ab + None, // q_ad + Some(10), // q_ad_max + Ignore, // q_fail + None, // c_genotype + None, // c_quality + None, // c_dp + Some(11), // c_ad + Some(Ignore), // expected, None = pass + )] + // all none + #[case( + None, // q_dp_het + None, // q_dp_hom + None, // q_gq + None, // q_ab + None, // q_ad + None, // q_ad_max + Ignore, // q_fail + None, // c_genotype + None, // c_quality + None, // c_dp + None, // c_ad + None, // expected, None = pass + )] + fn passes_for_sample( + #[case] q_dp_het: Option, + #[case] q_dp_hom: Option, + #[case] q_gq: Option, + #[case] q_ab: Option, + #[case] q_ad: Option, + #[case] q_ad_max: Option, + #[case] q_fail: FailChoice, + #[case] c_genotype: Option<&'static str>, + #[case] c_quality: Option, + #[case] c_dp: Option, + #[case] c_ad: Option, + #[case] expected: Option, + ) -> Result<(), anyhow::Error> { + let settings = QualitySettings { + dp_het: q_dp_het, + dp_hom: q_dp_hom, + gq: q_gq, + ab: q_ab, + ad: q_ad, + ad_max: q_ad_max, + fail: q_fail, + }; + let call_info = CallInfo { + genotype: c_genotype.map(|s| s.to_string()), + quality: c_quality, + dp: c_dp, + ad: c_ad, + ..Default::default() + }; + + assert_eq!( + super::passes_for_sample(&settings, &call_info), + expected, + "settings: {:?}, call info: {:?}", + settings, + call_info + ); + + Ok(()) + } +} diff --git a/src/seqvars/query/interpreter/regions_allowlist.rs b/src/seqvars/query/interpreter/regions_allowlist.rs new file mode 100644 index 00000000..0fcd4965 --- /dev/null +++ b/src/seqvars/query/interpreter/regions_allowlist.rs @@ -0,0 +1,85 @@ +use crate::seqvars::query::schema::{CaseQuery, GenomicRegion, Range, SequenceVariant}; + +/// Determine whether the `SequenceVariant` passes the regions allowlist filter. +pub fn passes(query: &CaseQuery, seqvar: &SequenceVariant) -> bool { + if let Some(region_allowlist) = &query.genomic_regions { + if region_allowlist.is_empty() { + true + } else { + let res = region_allowlist.iter().any(|region| { + overlaps( + region, + &seqvar.chrom, + seqvar.pos, + seqvar.pos + seqvar.reference.len() as i32 - 1, + ) + }); + if !res { + tracing::trace!( + "variant {:?} fails region allowlist filter {:?}", + seqvar, + ®ion_allowlist + ); + } + res + } + } else { + true + } +} + +fn overlaps(region: &GenomicRegion, seqvar_chrom: &str, seqvar_pos: i32, seqvar_end: i32) -> bool { + let GenomicRegion { + chrom: region_chrom, + range: region_range, + } = region; + + let region_chrom_c = annonars::common::cli::canonicalize(region_chrom); + let seqvar_chrom_c = annonars::common::cli::canonicalize(seqvar_chrom); + if region_chrom_c != seqvar_chrom_c { + return false; + } + + if let Some(Range { + start: region_start, + end: region_end, + }) = region_range + { + *region_start <= seqvar_end && *region_end >= seqvar_pos + } else { + true + } +} + +#[cfg(test)] +mod test { + use rstest::rstest; + + #[rstest] + #[case("1", Some((100, 200)), "1", 100, 200, true)] + #[case("chr1", Some((100, 200)), "1", 100, 200, true)] + #[case("chr1", Some((100, 200)), "chr1", 100, 200, true)] + #[case("chr1", Some((100, 200)), "chr1", 200, 300, true)] + #[case("chr1", Some((100, 200)), "chr1", 201, 300, false)] + #[case("1", Some((100, 200)), "2", 100, 200, false)] + fn overlaps( + #[case] region_chrom: &str, + #[case] region_range: Option<(i32, i32)>, + #[case] seqvar_chrom: &str, + #[case] seqvar_start: i32, + #[case] seqvar_end: i32, + #[case] expected: bool, + ) { + let region = super::GenomicRegion { + chrom: String::from(region_chrom), + range: region_range.map(|(region_start, region_end)| super::Range { + start: region_start, + end: region_end, + }), + }; + assert_eq!( + super::overlaps(®ion, seqvar_chrom, seqvar_start, seqvar_end), + expected + ); + } +} diff --git a/src/seqvars/query/mod.rs b/src/seqvars/query/mod.rs new file mode 100644 index 00000000..d67a7a07 --- /dev/null +++ b/src/seqvars/query/mod.rs @@ -0,0 +1,677 @@ +//! Code implementing the "seqvars query" sub command. + +pub mod annonars; +pub mod interpreter; +pub mod output; +pub mod schema; +pub mod sorting; + +use std::io::{BufRead, Write}; +use std::time::Instant; + +use clap::{command, Parser}; +use ext_sort::LimitedBufferBuilder; +use ext_sort::{ExternalSorter, ExternalSorterBuilder}; +use itertools::Itertools; +use noodles_vcf as vcf; + +use mehari::{annotate::seqvars::CHROM_TO_CHROM_NO, common::open_read_maybe_gz}; +use rand_core::{RngCore, SeedableRng}; +use thousands::Separable; +use uuid::Uuid; + +use crate::common; +use crate::seqvars::query::schema::GenotypeChoice; +use crate::{common::trace_rss_now, common::GenomeRelease}; + +use self::annonars::Annotator; +use self::schema::CaseQuery; +use self::schema::SequenceVariant; +use self::sorting::{ByCoordinate, ByHgncId}; + +/// Command line arguments for `seqvars query` sub command. +#[derive(Parser, Debug)] +#[command(author, version, about = "Run query for seqvars", long_about = None)] +pub struct Args { + /// Genome release to assume. + #[arg(long, value_enum)] + pub genome_release: GenomeRelease, + /// Result set ID. + #[arg(long)] + pub result_set_id: Option, + /// The case UUID. + #[arg(long)] + pub case_uuid_id: Option, + /// Path to worker database to use for querying. + #[arg(long)] + pub path_db: String, + /// Path to query JSON file. + #[arg(long)] + pub path_query_json: String, + /// Path to input TSV file. + #[arg(long)] + pub path_input: String, + /// Path to the output TSV file. + #[arg(long)] + pub path_output: String, + + /// Optional maximal number of total records to write out. + #[arg(long)] + pub max_results: Option, + /// Optional seed for RNG. + #[arg(long)] + pub rng_seed: Option, + /// Maximal distance to TAD to consider (unused, but required when loading database). + #[arg(long, default_value_t = 10_000)] + pub max_tad_distance: i32, +} + +/// Utility struct to store statistics about counts. +#[derive(Debug, Default)] +struct QueryStats { + pub count_passed: usize, + pub count_total: usize, + pub by_consequence: indexmap::IndexMap, +} + +/// Checks whether the variants pass through the query interpreter. +/// +/// This function is only relevant if the query uses recessive mode. +fn passes_for_gene( + query: &CaseQuery, + seqvars: &Vec, +) -> Result { + #[derive(Debug, Clone, PartialEq, Eq)] + enum Mode { + ComphetRecessive, + Recessive, + Other, + } + + let mut mode = Mode::Other; + let mut index_name = String::default(); + let mut parents = Vec::new(); + query + .genotype + .iter() + .for_each(|(sample_name, genotype_choice)| match genotype_choice { + Some(GenotypeChoice::ComphetIndex) => { + index_name = sample_name.clone(); + mode = Mode::ComphetRecessive; + } + Some(GenotypeChoice::RecessiveIndex) => { + index_name = sample_name.clone(); + mode = Mode::Recessive; + } + Some(GenotypeChoice::RecessiveParent) => { + parents.push(sample_name.clone()); + } + _ => (), + }); + + eprintln!( + "mode = {:?}, index_name = {:?}, parents = {:?}", + mode, &index_name, &parents + ); + + // No special handling for non-recessive mode. + if mode == Mode::Other { + return Ok(true); + } + + let mut seen_het_parents = Vec::new(); + for seqvar in seqvars { + // Get parsed index genotype. + let index_gt: common::Genotype = seqvar + .call_info + .get(&index_name) + .expect("no call info for index") + .genotype + .as_ref() + .expect("no GT for index") + .parse() + .map_err(|e| anyhow::anyhow!("could not parse index genotype: {}", e))?; + + eprintln!( + "seqvar = {:?}, index_gt = {:?}, mode = {:?}", + &seqvar, &index_gt, mode + ); + if mode == Mode::Recessive && index_gt == common::Genotype::HomAlt { + // if hom. recessive is allowed then we are done + return Ok(true); + } else if mode != Mode::Recessive && index_gt != common::Genotype::Het { + // it only makese sense to continue in recessive mode if the index is het. + return Ok(false); + } + + // Otherwise, the index must be Het and we have to check which parent is also het. + // At this point, only one parent can be het. + let parent_gts = parents + .iter() + .map(|parent_name| { + seqvar + .call_info + .get(parent_name) + .expect("no call info for parent") + .genotype + .as_ref() + .expect("no GT for parent") + .parse::() + }) + .collect::, _>>()?; + let het_parents = parents + .iter() + .zip(parent_gts.iter()) + .filter(|(_, gt)| **gt == common::Genotype::Het) + .map(|(name, _)| name.clone()) + .collect::>(); + assert!(het_parents.len() <= 1); + eprintln!("het_parents = {:?}", &het_parents); + if let Some(parent) = het_parents.first() { + if !seen_het_parents.contains(parent) { + seen_het_parents.push(parent.clone()); + } + } + + eprintln!("seen_het_parents = {:?}", &seen_het_parents); + + // If the number of seen het. parents is equal to the number of parents, we are done. + if seen_het_parents.len() == parents.len() { + return Ok(true); + } + } + + // one of the recessive modes was active and we did not find all parents + Ok(false) +} + +/// Run the `args.path_input` VCF file and run through the given `interpreter` writing to +/// `args.path_output`. +fn run_query( + interpreter: &interpreter::QueryInterpreter, + args: &Args, + annotator: &annonars::Annotator, + rng: &mut rand::rngs::StdRng, +) -> Result { + let tmp_dir = tempdir::TempDir::new("vfw")?; + + let chrom_to_chrom_no = &CHROM_TO_CHROM_NO; + let mut stats = QueryStats::default(); + + // Buffer for generating UUIDs. + let mut uuid_buf = [0u8; 16]; + + // Open VCF file, create reader, and read header. + let mut input_reader = open_read_maybe_gz(&args.path_input).map_err(|e| { + anyhow::anyhow!("could not open file {} for reading: {}", args.path_input, e) + })?; + let mut input_reader = vcf::Reader::new(&mut input_reader); + let input_header = input_reader.read_header()?; + + let path_unsorted = tmp_dir.path().join("unsorted.jsonl"); + let path_by_hgnc = tmp_dir.path().join("by_hgnc_filtered.jsonl"); + let path_by_coord = tmp_dir.path().join("by_coord.jsonl"); + + // Read through input records using the query interpreter as a filter and write to + // temporary file for unsorted records. + { + // Create temporary output file. + let mut tmp_unsorted = std::fs::File::create(&path_unsorted) + .map(std::io::BufWriter::new) + .map_err(|e| anyhow::anyhow!("could not create temporary unsorted file: {}", e))?; + + for input_record in input_reader.records(&input_header) { + stats.count_total += 1; + let record_seqvar = SequenceVariant::from_vcf(&input_record?, &input_header) + .map_err(|e| anyhow::anyhow!("could not parse VCF record: {}", e))?; + tracing::debug!("processing record {:?}", record_seqvar); + + if interpreter.passes(&record_seqvar, annotator)?.pass_all { + stats.count_passed += 1; + if let Some(ann) = record_seqvar.ann_fields.first() { + ann.consequences.iter().for_each(|csq| { + stats + .by_consequence + .entry(*csq) + .and_modify(|e| *e += 1) + .or_insert(1); + }) + } + writeln!( + tmp_unsorted, + "{}", + serde_json::to_string(&sorting::ByHgncId::from(record_seqvar))? + ) + .map_err(|e| anyhow::anyhow!("could not write record to unsorted: {}", e))?; + } + } + tmp_unsorted.flush().map_err(|e| { + anyhow::anyhow!("could not flush temporary output file unsorted: {}", e) + })?; + } + + let elem_count = 10_000; // at most 10k records in memory + + // Now: + // + // - sort the records by HGNC ID using external sorting + // - group by HGNC id + // - keep the groups where the recessive criteria are met according to query + // - write out the records again for later sorting by coordinate + { + let tmp_unsorted = std::fs::File::open(&path_unsorted) + .map(std::io::BufReader::new) + .map_err(|e| anyhow::anyhow!("could not open temporary unsorted file: {}", e))?; + let mut tmp_by_hgnc_filtered = std::fs::File::create(&path_by_hgnc) + .map(std::io::BufWriter::new) + .map_err(|e| { + anyhow::anyhow!("could not create temporary by_hgnc_filtered file: {}", e) + })?; + + let sorter: ExternalSorter = + ExternalSorterBuilder::new() + .with_tmp_dir(tmp_dir.as_ref()) + .with_buffer(LimitedBufferBuilder::new(elem_count, false)) + .build() + .map_err(|e| anyhow::anyhow!("problem creating external sorter: {}", e))?; + let sorted_iter = sorter + .sort(tmp_unsorted.lines().map(|res| { + Ok(serde_json::from_str(&res.expect("problem reading line")) + .expect("problem deserializing")) + })) + .map_err(|e| anyhow::anyhow!("problem sorting temporary unsorted file: {}", e))?; + + sorted_iter + .map(|res| res.expect("problem reading line after sorting by HGNC ID")) + .group_by(|by_hgnc_id| by_hgnc_id.hgnc_id.clone()) + .into_iter() + .map(|(_, group)| { + group + .map(|ByHgncId { seqvar, .. }| seqvar) + .collect::>() + }) + .filter(|seqvars| passes_for_gene(&interpreter.query, seqvars).unwrap()) + .for_each(|seqvars| { + seqvars.into_iter().for_each(|seqvar| { + writeln!( + tmp_by_hgnc_filtered, + "{}", + serde_json::to_string(&sorting::ByCoordinate::from(seqvar)).unwrap() + ) + .expect("could not write record to by_hgnc_filtered"); + }) + }); + tmp_by_hgnc_filtered.flush().map_err(|e| { + anyhow::anyhow!( + "could not flush temporary output file by_hgnc_filtered: {}", + e + ) + })?; + } + + // Finally: + // - sort surviving records by coordinate + // - generate payload with annotations + { + let tmp_by_hgnc_filtered = std::fs::File::open(&path_by_hgnc) + .map(std::io::BufReader::new) + .map_err(|e| { + anyhow::anyhow!("could not open temporary tmp_by_hgnc_filtered file: {}", e) + })?; + let mut tmp_by_coord = std::fs::File::create(&path_by_coord) + .map(std::io::BufWriter::new) + .map_err(|e| anyhow::anyhow!("could not create temporary by_coord file: {}", e))?; + + let sorter: ExternalSorter = + ExternalSorterBuilder::new() + .with_tmp_dir(tmp_dir.as_ref()) + .with_buffer(LimitedBufferBuilder::new(elem_count, false)) + .build() + .map_err(|e| anyhow::anyhow!("problem creating external sorter: {}", e))?; + let sorted_iter = sorter + .sort(tmp_by_hgnc_filtered.lines().map(|res| { + Ok(serde_json::from_str(&res.expect("problem reading line")) + .expect("problem deserializing")) + })) + .map_err(|e| anyhow::anyhow!("problem sorting temporary unsorted file: {}", e))?; + + sorted_iter + .map(|res| res.expect("problem reading line after sorting by HGNC ID")) + .for_each(|ByCoordinate { seqvar, .. }| { + writeln!(tmp_by_coord, "{}", serde_json::to_string(&seqvar).unwrap()) + .expect("could not write record to by_coord"); + }); + + tmp_by_coord.flush().map_err(|e| { + anyhow::anyhow!( + "could not flush temporary output file by_hgnc_filtered: {}", + e + ) + })?; + } + + // Finally, perform annotation of the record using the annonars library and write it + // in TSV format, ready for import into the database. However, in recessive mode, we + // have to do a second pass to properly collect compound heterozygous variants. + + let mut csv_writer = csv::WriterBuilder::new() + .has_headers(true) + .delimiter(b'\t') + .quote_style(csv::QuoteStyle::Never) + .from_path(&args.path_output)?; + + let tmp_by_coord = std::fs::File::open(&path_by_coord) + .map(std::io::BufReader::new) + .map_err(|e| anyhow::anyhow!("could not open temporary by_coord file: {}", e))?; + + for line in tmp_by_coord.lines() { + // get next line into a String + let line = if let Ok(line) = line { + line + } else { + anyhow::bail!("error reading line from input file") + }; + let seqvar: SequenceVariant = serde_json::from_str(&line).map_err(|e| { + anyhow::anyhow!( + "error parsing line from input file: {:?} (line: {:?})", + e, + &line + ) + })?; + + create_payload_and_write_record( + seqvar, + annotator, + chrom_to_chrom_no, + &mut csv_writer, + args, + rng, + &mut uuid_buf, + )?; + } + + Ok(stats) +} + +/// Create output payload and write the record to the output file. +fn create_payload_and_write_record( + seqvar: SequenceVariant, + annotator: &Annotator, + chrom_to_chrom_no: &CHROM_TO_CHROM_NO, + csv_writer: &mut csv::Writer, + args: &Args, + rng: &mut rand::rngs::StdRng, + uuid_buf: &mut [u8; 16], +) -> Result<(), anyhow::Error> { + let result_payload = output::PayloadBuilder::default() + .case_uuid(args.case_uuid_id.unwrap_or_default()) + .gene_related( + output::gene_related::Record::with_seqvar_and_annotator(&seqvar, annotator) + .map_err(|e| anyhow::anyhow!("problem creating gene-related payload: {}", e))?, + ) + .variant_related( + output::variant_related::Record::with_seqvar_and_annotator(&seqvar, annotator) + .map_err(|e| anyhow::anyhow!("problem creating variant-related payload: {}", e))?, + ) + .call_related( + output::call_related::Record::with_seqvar(&seqvar) + .map_err(|e| anyhow::anyhow!("problem creating call-related payload: {}", e))?, + ) + .build() + .map_err(|e| anyhow::anyhow!("could not build payload: {}", e))?; + eprintln!("result_payload = {:?}", &result_payload); + let start = seqvar.pos; + let end = start + seqvar.reference.len() as i32 - 1; + let bin = mehari::annotate::seqvars::binning::bin_from_range(start - 1, end)? as u32; + let SequenceVariant { + chrom: chromosome, + reference, + alternative, + .. + } = seqvar; + csv_writer + .serialize( + &output::RecordBuilder::default() + .smallvariantqueryresultset_id(args.result_set_id.clone().unwrap_or(".".into())) + .sodar_uuid(Uuid::from_bytes({ + rng.fill_bytes(uuid_buf); + *uuid_buf + })) + .release(match args.genome_release { + GenomeRelease::Grch37 => "GRCh37".into(), + GenomeRelease::Grch38 => "GRCh38".into(), + }) + .chromosome_no( + *chrom_to_chrom_no + .get(&chromosome) + .expect("invalid chromosome") as i32, + ) + .chromosome(chromosome) + .start(start) + .end(end) + .bin(bin) + .reference(reference) + .alternative(alternative) + .payload( + serde_json::to_string(&result_payload) + .map_err(|e| anyhow::anyhow!("could not serialize payload: {}", e))?, + ) + .build() + .map_err(|e| anyhow::anyhow!("could not build record: {}", e))?, + ) + .map_err(|e| anyhow::anyhow!("could not write record: {}", e))?; + Ok(()) +} + +/// Main entry point for `seqvars query` sub command. +pub fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), anyhow::Error> { + let before_anything = Instant::now(); + tracing::info!("args_common = {:?}", &args_common); + tracing::info!("args = {:?}", &args); + + // Initialize the random number generator from command line seed if given or local entropy + // source. + let mut rng = if let Some(rng_seed) = args.rng_seed { + rand::rngs::StdRng::seed_from_u64(rng_seed) + } else { + rand::rngs::StdRng::from_entropy() + }; + + tracing::info!("Loading query..."); + let query: schema::CaseQuery = + serde_json::from_reader(std::fs::File::open(&args.path_query_json)?)?; + tracing::info!( + "... done loading query = {}", + &serde_json::to_string(&query)? + ); + + tracing::info!("Loading worker databases..."); + let before_loading = Instant::now(); + let path_worker_db = format!("{}/worker", &args.path_db); + let in_memory_dbs = crate::strucvars::query::load_databases( + &path_worker_db, + args.genome_release, + args.max_tad_distance, + ) + .map_err(|e| { + anyhow::anyhow!( + "could not load worker databases from {}: {}", + path_worker_db, + e + ) + })?; + let annotator = annonars::Annotator::with_path(&args.path_db, args.genome_release)?; + tracing::info!( + "...done loading databases in {:?}", + before_loading.elapsed() + ); + + trace_rss_now(); + + tracing::info!("Translating gene allow list..."); + let hgnc_allowlist = if let Some(gene_allowlist) = &query.gene_allowlist { + if gene_allowlist.is_empty() { + None + } else { + Some(crate::strucvars::query::translate_gene_allowlist( + gene_allowlist, + &in_memory_dbs, + )) + } + } else { + None + }; + + tracing::info!("Running queries..."); + let before_query = Instant::now(); + let query_stats = run_query( + &interpreter::QueryInterpreter::new(query, hgnc_allowlist), + args, + &annotator, + &mut rng, + )?; + tracing::info!("... done running query in {:?}", before_query.elapsed()); + tracing::info!( + "summary: {} records passed out of {}", + query_stats.count_passed.separate_with_commas(), + query_stats.count_total.separate_with_commas() + ); + tracing::info!("passing records by effect type"); + for (effect, count) in query_stats.by_consequence.iter() { + tracing::info!("{:?} -- {}", effect, count); + } + + trace_rss_now(); + + tracing::info!( + "All of `seqvars query` completed in {:?}", + before_anything.elapsed() + ); + Ok(()) +} + +#[cfg(test)] +mod test { + use rstest::rstest; + + use super::schema::{CallInfo, SequenceVariant}; + use crate::seqvars::query::schema::{CaseQuery, GenotypeChoice}; + + #[rstest] + #[case( + GenotypeChoice::ComphetIndex, + vec!["0/1,0/1,0/0"], + false, + )] + #[case( + GenotypeChoice::ComphetIndex, + vec!["1/1,0/0,0/0"], + false, + )] + #[case( + GenotypeChoice::ComphetIndex, + vec!["0/1,0/1,0/0","0/1,0/0,0/1"], + true, + )] + #[case( + GenotypeChoice::RecessiveIndex, + vec!["1/1,0/0,0/0","0/1,0/0,0/1"], + true, + )] + #[case( + GenotypeChoice::RecessiveIndex, + vec!["1/0,1/0,0/0","0/1,0/0,0/1"], + true, + )] + #[case( + GenotypeChoice::RecessiveIndex, + vec!["1/0,1/0,0/0","1/0,0/1,0/0"], + false, + )] + fn passes_for_gene_full_trio( + #[case] gt_choice_index: GenotypeChoice, + #[case] trio_gts: Vec<&str>, + #[case] passes: bool, + ) -> Result<(), anyhow::Error> { + let query = CaseQuery { + genotype: vec![ + ("index".into(), Some(gt_choice_index)), + ("father".into(), Some(GenotypeChoice::RecessiveParent)), + ("mother".into(), Some(GenotypeChoice::RecessiveParent)), + ] + .into_iter() + .collect(), + ..Default::default() + }; + let seqvars = trio_gts + .iter() + .map(|gts| { + let gts: Vec<&str> = gts.split(',').collect(); + SequenceVariant { + call_info: vec![ + ( + String::from("index"), + CallInfo { + genotype: Some(gts[0].into()), + ..Default::default() + }, + ), + ( + String::from("father"), + CallInfo { + genotype: Some(gts[1].into()), + ..Default::default() + }, + ), + ( + String::from("mother"), + CallInfo { + genotype: Some(gts[2].into()), + ..Default::default() + }, + ), + ] + .into_iter() + .collect(), + ..Default::default() + } + }) + .collect::>(); + + assert_eq!(super::passes_for_gene(&query, &seqvars)?, passes); + + Ok(()) + } + + #[tracing_test::traced_test] + #[rstest::rstest] + #[case("tests/seqvars/query/Case_1.ingested.vcf")] + #[case("tests/seqvars/query/dragen.ingested.vcf")] + fn smoke_test(#[case] path_input: &str) -> Result<(), anyhow::Error> { + mehari::common::set_snapshot_suffix!("{}", path_input.split('/').last().unwrap()); + + let tmpdir = temp_testdir::TempDir::default(); + let path_output = format!("{}/out.tsv", tmpdir.to_string_lossy()); + let path_input: String = path_input.into(); + let path_query_json = path_input.replace(".ingested.vcf", ".query.json"); + + let args_common = Default::default(); + let args = super::Args { + genome_release: crate::common::GenomeRelease::Grch37, + path_db: "tests/seqvars/query/db".into(), + path_query_json, + path_input, + path_output, + max_results: None, + rng_seed: Some(42), + max_tad_distance: 10_000, + result_set_id: None, + case_uuid_id: None, + }; + super::run(&args_common, &args)?; + + insta::assert_snapshot!(std::fs::read_to_string(args.path_output.as_str())?); + + Ok(()) + } +} diff --git a/src/seqvars/query/output/call_related.rs b/src/seqvars/query/output/call_related.rs new file mode 100644 index 00000000..2e6aa5dd --- /dev/null +++ b/src/seqvars/query/output/call_related.rs @@ -0,0 +1,50 @@ +//! Call-related information. + +use crate::seqvars::query::schema::SequenceVariant; + +/// Call-related record. +#[derive(Debug, Default, Clone, serde::Serialize, serde::Deserialize, derive_new::new)] +pub struct Record { + /// The genotype information for each sample. + pub call_info: indexmap::IndexMap, +} + +impl Record { + /// Construct a new `Record` from a `SequenceVariant`. + /// + /// # Error + /// + /// Returns an error if the `SequenceVariant` does not contain all necessary information. + pub fn with_seqvar(seqvar: &SequenceVariant) -> Result { + Ok(Self { + call_info: seqvar + .call_info + .iter() + .map(|(sample_name, call_info)| { + ( + sample_name.clone(), + CallInfo::new( + call_info.dp, + call_info.ad, + call_info.quality.map(|q| q as i32), + call_info.genotype.clone(), + ), + ) + }) + .collect(), + }) + } +} + +/// Genotype information. +#[derive(Debug, Default, Clone, serde::Serialize, serde::Deserialize, derive_new::new)] +pub struct CallInfo { + /// Depth of coverage. + pub dp: Option, + /// Alternate read depth. + pub ad: Option, + /// Genotype quality. + pub gq: Option, + /// Genotype. + pub gt: Option, +} diff --git a/src/seqvars/query/output/gene_related.rs b/src/seqvars/query/output/gene_related.rs new file mode 100644 index 00000000..1c9b341a --- /dev/null +++ b/src/seqvars/query/output/gene_related.rs @@ -0,0 +1,151 @@ +//! Gene-related information for the gene. + +use mehari::annotate::seqvars::ann::Consequence; + +use crate::seqvars::query::{annonars::Annotator, schema::SequenceVariant}; + +/// Gene-related information for a `ResultPayload`. +#[derive(Debug, Default, Clone, serde::Serialize, serde::Deserialize, derive_new::new)] +pub struct Record { + /// Gene identity related (for display of gene symbol). + pub identity: Identity, + /// Gene-related consequences of a variant. + pub consequences: Consequences, + /// Phenotype-related information, if any. + #[serde(skip_serializing_if = "Option::is_none")] + pub phenotype: Option, + /// Gene-wise constraints on the gene, if any. + #[serde(skip_serializing_if = "Option::is_none")] + pub constraints: Option, +} + +impl Record { + /// Construct given a `SequenceVariant` if the information is given in the annotation. + /// + /// Note that we will only look at the first annotation record as the ingest creates + /// one `SequenceVariant` record per gene. + /// + /// # Error + /// + /// Returns an error if `seqvar` does not contain all necessary information. + pub fn with_seqvar_and_annotator( + seqvar: &SequenceVariant, + annotator: &Annotator, + ) -> Result, anyhow::Error> { + if let Some(ann) = seqvar.ann_fields.first() { + let hgnc_id = ann.gene_id.clone(); + + let gene_record = annotator + .query_genes(&hgnc_id) + .map_err(|e| anyhow::anyhow!("problem querying genes database: {}", e))?; + + if !ann.gene_id.is_empty() && !ann.gene_symbol.is_empty() { + return Ok(Some(Self { + identity: Identity::new(hgnc_id, ann.gene_symbol.clone()), + consequences: Consequences::new( + ann.hgvs_t + .clone() + .ok_or_else(|| anyhow::anyhow!("missing hgvs_t annotation"))?, + ann.hgvs_p.clone(), + ann.consequences.clone(), + ), + phenotype: gene_record.as_ref().map(Phenotype::with_gene_record), + constraints: gene_record.as_ref().and_then(|gene_record| { + gene_record + .gnomad_constraints + .as_ref() + .map(|gnomad_constraints| { + Constraints::with_constraints_record(gnomad_constraints) + }) + }), + })); + } + } + Ok(None) + } +} + +/// Result information for gene identity. +#[derive(Debug, Default, Clone, serde::Serialize, serde::Deserialize, derive_new::new)] +pub struct Identity { + /// HGNC gene ID. + pub hgnc_id: String, + /// HGNC gene symbol. + pub hgnc_symbol: String, +} + +/// Result information related to phenotype / disease. +#[derive(Debug, Default, Clone, serde::Serialize, serde::Deserialize, derive_new::new)] +pub struct Phenotype { + /// Whether the gene is on the ACMG supplementary finding list. + pub is_acmg_sf: bool, + /// Whether the gene is a known disease gene. + pub is_disease_gene: bool, +} + +impl Phenotype { + /// Construct given a `genes` database record. + pub fn with_gene_record(gene_record: &annonars::genes::pbs::Record) -> Self { + Self { + is_acmg_sf: gene_record.acmg_sf.is_some(), + is_disease_gene: gene_record.omim.is_some() || gene_record.orpha.is_some(), + } + } +} + +/// Consequences related to a gene. +#[derive(Debug, Default, Clone, serde::Serialize, serde::Deserialize, derive_new::new)] +pub struct Consequences { + /// HGVS.{c,n} code of variant + pub hgvs_t: String, + /// HGVS.p code of variant + #[serde(skip_serializing_if = "Option::is_none")] + pub hgvs_p: Option, + + /// The predicted variant consequences. + #[serde(skip_serializing_if = "Vec::is_empty")] + pub consequences: Vec, +} + +/// Result gene constraint information. +#[allow(clippy::too_many_arguments)] +#[derive(Debug, Default, Clone, serde::Serialize, serde::Deserialize, derive_new::new)] +pub struct Constraints { + /// gnomAD mis_z score + pub gnomad_mis_z: f32, + /// gnomAD oe_lof score + pub gnomad_oe_lof: f32, + /// gnomAD oe_lof_lower score + pub gnomad_oe_lof_lower: f32, + /// gnomAD oe_lof_upper score (LOEF) + pub gnomad_oe_lof_upper: f32, + /// gnomAD oe_mis score + pub gnomad_oe_mis: f32, + /// gnomAD oe_mis_lower score + pub gnomad_oe_mis_lower: f32, + /// gnomAD oe_mis_upper score + pub gnomad_oe_mis_upper: f32, + /// gnomAD pLI score + pub gnomad_pli: f32, + /// gnomAD syn_z score + pub gnomad_syn_z: f32, +} + +impl Constraints { + /// Construct given a `genes` database record. + pub fn with_constraints_record( + constraints: &annonars::genes::pbs::GnomadConstraintsRecord, + ) -> Self { + Self { + gnomad_mis_z: constraints.mis_z.unwrap_or_default() as f32, + gnomad_oe_lof: constraints.oe_lof.unwrap_or_default() as f32, + gnomad_oe_lof_lower: constraints.oe_lof_lower.unwrap_or_default() as f32, + gnomad_oe_lof_upper: constraints.oe_lof_upper.unwrap_or_default() as f32, + gnomad_oe_mis: constraints.oe_mis.unwrap_or_default() as f32, + gnomad_oe_mis_lower: constraints.oe_mis_lower.unwrap_or_default() as f32, + gnomad_oe_mis_upper: constraints.oe_mis_upper.unwrap_or_default() as f32, + gnomad_pli: constraints.pli.unwrap_or_default() as f32, + gnomad_syn_z: constraints.syn_z.unwrap_or_default() as f32, + } + } +} diff --git a/src/seqvars/query/output/mod.rs b/src/seqvars/query/output/mod.rs new file mode 100644 index 00000000..d89a86d3 --- /dev/null +++ b/src/seqvars/query/output/mod.rs @@ -0,0 +1,52 @@ +//! Data structureds for writing the output. + +pub mod gene_related; +pub mod variant_related; + +pub mod call_related; + +/// A result record from the query. +/// +/// These records are written to TSV for import into the database. They contain the +/// bare necessary information for sorting etc. in the database. The actual main +/// data is in the payload, serialized as JSON. +#[derive(Debug, Default, Clone, serde::Serialize, serde::Deserialize, derive_builder::Builder)] +pub struct Record { + /// UUID for the record. + pub sodar_uuid: uuid::Uuid, + /// Genome release for the coordinate. + pub release: String, + /// Chromosome name. + pub chromosome: String, + /// Chromosome number. + pub chromosome_no: i32, + /// Reference allele sequence. + pub reference: String, + /// Alternative allele sequence. + pub alternative: String, + /// UCSC bin of the record. + pub bin: u32, + /// Start position of the record. + pub start: i32, + /// End position of the record. + pub end: i32, + /// The result set ID as specified on the command line. + pub smallvariantqueryresultset_id: String, + /// The JSON-serialized `ResultPayload`. + pub payload: String, +} + +/// The structured result information of the result record. +#[derive(Debug, Default, Clone, serde::Serialize, serde::Deserialize, derive_builder::Builder)] +pub struct Payload { + /// Case UUID as specified on the command line. + pub case_uuid: uuid::Uuid, + /// The affected gene and consequence, if any. + #[serde(skip_serializing_if = "Option::is_none")] + pub gene_related: Option, + /// Variant-related information, always present. + #[serde(skip_serializing_if = "variant_related::Record::is_empty")] + pub variant_related: variant_related::Record, + /// Genotypes call related, always present. + pub call_related: call_related::Record, +} diff --git a/src/seqvars/query/output/variant_related.rs b/src/seqvars/query/output/variant_related.rs new file mode 100644 index 00000000..8ce08370 --- /dev/null +++ b/src/seqvars/query/output/variant_related.rs @@ -0,0 +1,488 @@ +//! Variant-related information. + +use crate::seqvars::query::{ + annonars::Annotator, + output::variant_related::score_collection::{ + Collector, ExtremalValueCollector, SingleValueCollector, + }, + schema::SequenceVariant, +}; + +/// Helper modules for score collection. +pub mod score_collection { + /// Trait for score collection. + pub trait Collector { + /// Return column names of interest. + fn column_names(&self) -> Vec; + /// Register one column value. + fn register(&mut self, column_name: &str, value: &serde_json::Value); + /// Write collected scores to the given `indexmap::IndexMap``. + fn write_to(&self, dict: &mut indexmap::IndexMap); + } + + /// Simple implementation for collecting a single score. + #[derive(Debug, Clone)] + pub struct SingleValueCollector { + /// The column name to collect. + pub input_column_name: String, + /// The output column name. + pub output_column_name: String, + /// The collected value, if any. + pub value: Option, + } + + impl SingleValueCollector { + /// Construct given column name. + pub fn new(input_column_name: &str, output_column_name: &str) -> Self { + Self { + input_column_name: input_column_name.into(), + output_column_name: output_column_name.into(), + value: None, + } + } + } + + impl Collector for SingleValueCollector { + fn column_names(&self) -> Vec { + vec![self.input_column_name.clone()] + } + + fn register(&mut self, column_name: &str, value: &serde_json::Value) { + if column_name == self.input_column_name && !value.is_null() { + self.value = Some(value.clone()); + } + } + + fn write_to(&self, dict: &mut indexmap::IndexMap) { + if let Some(value) = self.value.as_ref() { + dict.insert(self.input_column_name.clone(), value.clone()); + } + } + } + + /// Simple implementation for collecting aggregated min/max score. + #[derive(Debug, Clone)] + pub struct ExtremalValueCollector { + /// Whether is max (else is min). + pub is_max: bool, + /// The output column name. + pub output_column_name: String, + /// The column names to collect. + pub column_names: Vec, + /// The collected values, if any. + pub values: indexmap::IndexMap, + } + + impl ExtremalValueCollector { + /// Construct given column name. + pub fn new(column_names: &[&str], output_column_name: &str, is_max: bool) -> Self { + Self { + is_max, + output_column_name: output_column_name.to_string(), + column_names: column_names.iter().map(|s| s.to_string()).collect(), + values: Default::default(), + } + } + } + + impl Collector for ExtremalValueCollector { + fn column_names(&self) -> Vec { + self.column_names.clone() + } + + fn register(&mut self, column_name: &str, value: &serde_json::Value) { + if self.column_names.iter().any(|s| s.as_str() == column_name) && !value.is_null() { + self.values.insert(column_name.to_string(), value.clone()); + } + } + + fn write_to(&self, dict: &mut indexmap::IndexMap) { + let mut sel_name = None; + let mut sel_value = serde_json::Value::Null; + for (name, value) in self.values.iter() { + if value.is_null() || !value.is_number() { + // can only select numeric values that are not null + continue; + } + + if sel_value.is_null() + || (self.is_max + && value.as_f64().unwrap_or_default() + > sel_value.as_f64().unwrap_or_default()) + || (!self.is_max + && value.as_f64().unwrap_or_default() + < sel_value.as_f64().unwrap_or_default()) + { + sel_name = Some(name.clone()); + sel_value = value.clone(); + } + } + + if let Some(sel_name) = sel_name { + dict.insert(self.output_column_name.clone(), sel_value); + dict.insert( + format!("{}_argmax", self.output_column_name), + serde_json::Value::String(sel_name), + ); + } + } + } +} + +/// Simple + +/// Record for variant-related scores. +#[derive(Debug, Default, Clone, serde::Serialize, serde::Deserialize, derive_new::new)] +pub struct Record { + /// Precomputed scores. + #[serde(skip_serializing_if = "indexmap::IndexMap::is_empty")] + pub precomputed_scores: indexmap::IndexMap, + /// Database identifiers. + #[serde(skip_serializing_if = "DbIds::is_empty")] + pub db_ids: DbIds, + /// Clinvar information. + #[serde(skip_serializing_if = "Option::is_none")] + pub clinvar: Option, + /// Frequency information. + #[serde(skip_serializing_if = "Frequency::is_empty")] + pub frequency: Frequency, +} + +impl Record { + /// Construct given sequence variant and annonars annotator. + pub fn with_seqvar_and_annotator( + seqvar: &SequenceVariant, + annotator: &Annotator, + ) -> Result { + Ok(Self { + precomputed_scores: Self::query_precomputed_scores(seqvar, annotator)?, + db_ids: DbIds::with_seqvar_and_annotator(seqvar, annotator)?, + clinvar: Clinvar::with_seqvar_and_annotator(seqvar, annotator)?, + frequency: Frequency::with_seqvar(seqvar)?, + }) + } + + /// Query precomputed scores for `seqvar` from annonars `annotator`. + pub fn query_precomputed_scores( + seqvar: &SequenceVariant, + annotator: &Annotator, + ) -> Result, anyhow::Error> { + let mut result = indexmap::IndexMap::new(); + + // Extract values from CADD. + if let Some(cadd_values) = annotator + .query_cadd(seqvar) + .as_ref() + .map_err(|e| anyhow::anyhow!("problem querying CADD: {}", e))? + { + let mut collectors: Vec> = vec![ + Box::new(SingleValueCollector::new("PHRED", "cadd_phred")), + Box::new(SingleValueCollector::new("SIFTval", "sift")), + Box::new(SingleValueCollector::new("PolyPhenVal", "polyphen")), + Box::new(ExtremalValueCollector::new( + &[ + "SpliceAI-acc-gain", + "SpliceAI-acc-loss", + "SpliceAI-don-gain", + "SpliceAI-don-loss", + ], + "spliceai", + true, + )), + ]; + + for (column, value) in annotator + .annonars_dbs + .cadd_ctx + .schema + .columns + .iter() + .zip(cadd_values.iter()) + { + for collector in collectors.iter_mut() { + collector.register(column.name.as_str(), value); + } + } + + collectors.iter_mut().for_each(|collector| { + collector.write_to(&mut result); + }) + } + + // Extract values from dbNSFP + + if let Some(dbnsfp_values) = annotator + .query_dbnsfp(seqvar) + .as_ref() + .map_err(|e| anyhow::anyhow!("problem querying dbNSFP: {}", e))? + { + // REVEL_score + // BayesDel_addAF_score + let mut collectors: Vec> = vec![ + Box::new(SingleValueCollector::new("REVEL_score", "revel")), + Box::new(SingleValueCollector::new( + "BayesDel_addAF_score", + "bayesel_addaf", + )), + ]; + + for (column, value) in annotator + .annonars_dbs + .cadd_ctx + .schema + .columns + .iter() + .zip(dbnsfp_values.iter()) + { + for collector in collectors.iter_mut() { + collector.register(column.name.as_str(), value); + } + } + + collectors.iter_mut().for_each(|collector| { + collector.write_to(&mut result); + }) + } + + Ok(result) + } + + /// Returns whether all fields are empty and would not be serialized. + pub fn is_empty(&self) -> bool { + self.precomputed_scores.is_empty() + && self.db_ids.is_empty() + && self.clinvar.is_none() + && self.frequency.is_empty() + } +} + +/// Database identifiers. +#[derive(Debug, Default, Clone, serde::Serialize, serde::Deserialize, derive_new::new)] +pub struct DbIds { + /// The variant's dbSNP identifier present. + #[serde(skip_serializing_if = "Option::is_none")] + pub dbsnp_rs: Option, +} + +impl DbIds { + /// Construct given sequence variant and annonars annotator. + pub fn with_seqvar_and_annotator( + seqvar: &SequenceVariant, + annotator: &Annotator, + ) -> Result { + Ok(Self { + dbsnp_rs: annotator + .query_dbsnp(seqvar) + .map_err(|e| anyhow::anyhow!("problem querying dbSNP: {}", e))? + .map(|record| format!("rs{}", record.rs_id)), + }) + } + + /// Returns whether all database identifiers are unset. + pub fn is_empty(&self) -> bool { + self.dbsnp_rs.is_none() + } +} + +/// ClinVar-related information. +#[derive(Debug, Default, Clone, serde::Serialize, serde::Deserialize, derive_new::new)] +pub struct Clinvar { + /// The VCV accession. + pub vcv: String, + /// The RCV accession. + pub rcv: String, + /// The clinical significance. + pub significance: String, + /// The review status. + pub review_status: String, +} + +impl Clinvar { + /// Construct given sequence variant and annonars annotator. + pub fn with_seqvar_and_annotator( + seqvar: &SequenceVariant, + annotator: &Annotator, + ) -> Result, anyhow::Error> { + annotator + .query_clinvar_minimal(seqvar) + .map_err(|e| anyhow::anyhow!("problem querying clinvar-minimal: {}", e))? + .map(|record| { + if let Some(assertion) = record.reference_assertions.first() { + let annonars::clinvar_minimal::pbs::ReferenceAssertion { + rcv, + clinical_significance, + review_status, + .. + } = assertion; + Ok(Self { + vcv: record.vcv.clone(), + rcv: rcv.clone(), + significance: match clinical_significance { + 0 => "Pathogenic", + 1 => "Likely pathogenic", + 2 => "Uncertain significance", + 3 => "Likely benign", + 4 => "Benign", + _ => anyhow::bail!( + "invalid clinical significance enum: {}", + clinical_significance + ), + } + .into(), + review_status: match review_status { + 0 => "practice guideline", + 1 => "reviewed by expert panel", + 2 => "criteria provided, multiple submitters, no conflicts", + 3 => "criteria provided, single submitter", + 4 => "criteria provided, conflicting interpretations", + 5 => "no assertion criteria provided", + 6 => "no assertion provided", + _ => anyhow::bail!("invalid review status enum: {}", review_status), + } + .into(), + }) + } else { + unreachable!("no reference clinvar assertion") + } + }) + .transpose() + } +} + +/// Frequency information. +#[derive(Debug, Default, Clone, serde::Serialize, serde::Deserialize, derive_builder::Builder)] +pub struct Frequency { + /// gnomAD-genomes frequency + #[serde(skip_serializing_if = "Option::is_none")] + #[builder(default)] + pub gnomad_genomes: Option, + /// gnomAD-exomes frequency + #[serde(skip_serializing_if = "Option::is_none")] + #[builder(default)] + pub gnomad_exomes: Option, + /// gnomad-mtDNA frequency + #[serde(skip_serializing_if = "Option::is_none")] + #[builder(default)] + pub gnomad_mtdna: Option, + /// HelixMtDb frequency + #[serde(skip_serializing_if = "Option::is_none")] + #[builder(default)] + pub helixmtdb: Option, + /// inhouse frequency + #[serde(skip_serializing_if = "Option::is_none")] + #[builder(default)] + pub inhouse: Option, +} + +impl Frequency { + /// Extract frequency information from `seqvar` + pub fn with_seqvar(seqvar: &SequenceVariant) -> Result { + let chrom = annonars::common::cli::canonicalize(&seqvar.chrom); + let frequency = if chrom == "MT" { + FrequencyBuilder::default() + .gnomad_genomes( + NuclearFrequency::new( + seqvar.gnomad_genomes_af(), + seqvar.gnomad_genomes_an, + seqvar.gnomad_genomes_het, + seqvar.gnomad_genomes_hom, + seqvar.gnomad_genomes_hemi, + ) + .some_unless_empty(), + ) + .gnomad_exomes( + NuclearFrequency::new( + seqvar.gnomad_exomes_af(), + seqvar.gnomad_exomes_an, + seqvar.gnomad_exomes_het, + seqvar.gnomad_exomes_hom, + seqvar.gnomad_exomes_hemi, + ) + .some_unless_empty(), + ) + .build() + } else { + FrequencyBuilder::default() + .gnomad_mtdna( + MtdnaFrequency::new( + seqvar.gnomad_genomes_af(), + seqvar.gnomad_genomes_an, + seqvar.gnomad_genomes_het, + seqvar.gnomad_genomes_hom, + ) + .some_unless_empty(), + ) + .helixmtdb( + MtdnaFrequency::new( + seqvar.helixmtdb_af(), + seqvar.helix_an, + seqvar.helix_het, + seqvar.helix_hom, + ) + .some_unless_empty(), + ) + .build() + } + .map_err(|e| anyhow::anyhow!("could not build frequency information: {}", e))?; + Ok(frequency) + } + + /// Returns whether all frequencies are empty. + pub fn is_empty(&self) -> bool { + self.gnomad_genomes.is_none() + && self.gnomad_exomes.is_none() + && self.gnomad_mtdna.is_none() + && self.helixmtdb.is_none() + && self.inhouse.is_none() + } +} + +/// Nuclear frequency information. +#[derive(Debug, Default, Clone, serde::Serialize, serde::Deserialize, derive_new::new)] +pub struct NuclearFrequency { + /// Overall allele frequency. + pub allele_freq: f32, + /// Number of alleles. + pub allele_count: i32, + /// Number of heterozygous carriers. + pub het_carriers: i32, + /// Number of homozygous carriers. + pub hom_carriers: i32, + /// Number of hemizygous carriers. + pub hemi_carriers: i32, +} + +impl NuclearFrequency { + /// Return self or None if empty. + pub fn some_unless_empty(self) -> Option { + if self.allele_count == 0 { + None + } else { + Some(self) + } + } +} + +/// Mitochondrial frequency information. +#[derive(Debug, Default, Clone, serde::Serialize, serde::Deserialize, derive_new::new)] +pub struct MtdnaFrequency { + /// Overall allele frequency. + pub allele_freq: f32, + /// Number of alleles. + pub allele_count: i32, + /// Number of heterplasmic carriers. + pub het_carriers: i32, + /// Number of homoplasmic carriers. + pub hom_carriers: i32, +} + +impl MtdnaFrequency { + /// Return self or None if empty. + pub fn some_unless_empty(self) -> Option { + if self.allele_count == 0 { + None + } else { + Some(self) + } + } +} diff --git a/src/seqvars/query/schema.rs b/src/seqvars/query/schema.rs new file mode 100644 index 00000000..469f6617 --- /dev/null +++ b/src/seqvars/query/schema.rs @@ -0,0 +1,664 @@ +//! Supporting code for seqvar query definition. + +use noodles_vcf as vcf; + +/// Enumeration for recessive mode queries. +#[derive( + serde::Serialize, serde::Deserialize, PartialEq, Eq, PartialOrd, Ord, Hash, Debug, Clone, Copy, +)] +pub enum RecessiveMode { + /// Recessive. + #[serde(rename = "recessive")] + Recessive, + /// Compound recessive. + #[serde(rename = "compound-recessive")] + CompoundRecessive, +} + +/// Choices for failing quality thresholds on genotypes. +#[derive( + serde::Serialize, + serde::Deserialize, + PartialEq, + Eq, + PartialOrd, + Ord, + Hash, + Debug, + Clone, + Copy, + Default, +)] +pub enum FailChoice { + /// Ignore failure. + #[default] + #[serde(rename = "ignore")] + Ignore, + /// Drop whole variant. + #[serde(rename = "drop-variant")] + Drop, + /// Interpret as "no-call". + #[serde(rename = "no-call")] + NoCall, +} + +/// Choice for genotype. +#[derive( + serde::Serialize, + serde::Deserialize, + PartialEq, + Eq, + PartialOrd, + Ord, + Hash, + Debug, + Clone, + Copy, + Default, +)] +pub enum GenotypeChoice { + /// Any genotype. + #[default] + #[serde(rename = "any")] + Any, + /// Ref. genotype. + #[serde(rename = "ref")] + Ref, + /// Het. genotype. + #[serde(rename = "het")] + Het, + /// Hom. genotype. + #[serde(rename = "hom")] + Hom, + /// Non-hom. genotype. + #[serde(rename = "non-hom")] + NonHom, + /// Variant genotype. + #[serde(rename = "variant")] + Variant, + /// Index in comp. het. recessive inheritance. + #[serde(rename = "comphet-index")] + ComphetIndex, + /// Index in recessive inheritance. + #[serde(rename = "recessive-index")] + RecessiveIndex, + /// Parent in recessive inheritance. + #[serde(rename = "recessive-parent")] + RecessiveParent, +} + +impl GenotypeChoice { + /// Return wehther the genotype choice matches the genotype string. + /// + /// Note that we assume properly ingested VCFs with only one alternate allele. + /// The valid genotype strings have the form "/", "|" or + /// "" with "" being one of "0", "1", and ".". + pub fn matches(&self, gt_str: &str) -> Result { + Ok(match self { + GenotypeChoice::Any => true, + GenotypeChoice::Ref => ["0", "0|0", "0/0"].contains(>_str), + GenotypeChoice::Het => ["0/1", "0|1", "1/0", "1|0"].contains(>_str), + GenotypeChoice::Hom => ["1", "1/1", "1|1"].contains(>_str), + GenotypeChoice::NonHom => !["1", "1/1", "1|1"].contains(>_str), + GenotypeChoice::Variant => { + ["1", "0/1", "0|1", "1/0", "1|0", "1|1", "1/1"].contains(>_str) + } + GenotypeChoice::ComphetIndex + | GenotypeChoice::RecessiveIndex + | GenotypeChoice::RecessiveParent => { + anyhow::bail!("recessive marker is not a genotype choice") + } + }) + } +} + +/// Quality settings for one sample. +#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)] +pub struct QualitySettings { + /// Minimal coverage for het. sites. + pub dp_het: Option, + /// Minimal coverage for hom. sites. + pub dp_hom: Option, + /// Minimal genotype quality. + pub gq: Option, + /// Minimal allele balance for het. variants. + pub ab: Option, + /// Minimal number of alternate reads. + pub ad: Option, + /// Maximal number of alternate reads + pub ad_max: Option, + /// Behaviour on failing quality thresholds. + pub fail: FailChoice, +} + +/// Data structure to hold a range. +#[derive( + serde::Serialize, serde::Deserialize, PartialEq, Eq, PartialOrd, Ord, Hash, Debug, Clone, +)] +pub struct Range { + /// Start of range. + pub start: i32, + /// End of range. + pub end: i32, +} + +/// Data struture to hold a genomic region. +#[derive( + serde::Serialize, serde::Deserialize, PartialEq, Eq, PartialOrd, Ord, Hash, Debug, Clone, +)] +pub struct GenomicRegion { + /// Chromosome. + pub chrom: String, + /// Range of region. + pub range: Option, +} + +/// Data structure with a single query. +#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone)] +#[serde(default)] +pub struct CaseQuery { + /// Molecular consequences to consider. + pub consequences: Vec, + + /// Quality settings for each individual. + pub quality: indexmap::IndexMap, + /// Genotype choice for each individual. + pub genotype: indexmap::IndexMap>, + + /// Whether to include coding transcripts. + pub transcripts_coding: bool, + /// Whether to include non-coding transcripts. + pub transcripts_noncoding: bool, + + /// Whether to include SNVs. + pub var_type_snv: bool, + /// Whether to include indels. + pub var_type_indel: bool, + /// Whether to include MNVs. + pub var_type_mnv: bool, + + /// Maximal distance to next exon, if any. + pub max_exon_dist: Option, + + /// List of HGNC symbols, HGNC:s, ENSGs, or NCBI Gene IDs to restrict + /// the resulting variants to. + pub gene_allowlist: Option>, + /// List of genomic regions to limit restrict the resulting variants to. + pub genomic_regions: Option>, + + /// Wether to require ClinVar membership. + pub require_in_clinvar: bool, + /// Whether to include benign ClinVar variants. + pub clinvar_include_benign: bool, + /// Whether to include pathogenic ClinVar variants. + pub clinvar_include_pathogenic: bool, + /// Whether to include likely benign ClinVar variants. + pub clinvar_include_likely_benign: bool, + /// Whether to include likely pathogenic ClinVar variants. + pub clinvar_include_likely_pathogenic: bool, + /// Whether to include uncertain significance ClinVar variants. + pub clinvar_include_uncertain_significance: bool, + + /// Whether to enable filtration by gnomAD exomes. + pub gnomad_exomes_enabled: bool, + /// Whether to enable filtration by gnomAD genomes + pub gnomad_genomes_enabled: bool, + /// Whether to enable filtration by 1000 Genomes. + pub inhouse_enabled: bool, + /// Whether to enable filtration by mtDB. + pub helixmtdb_enabled: bool, + + /// Maximal frequency in gnomAD exomes. + pub gnomad_exomes_frequency: Option, + /// Maximal number of heterozygous carriers in gnomAD exomes. + pub gnomad_exomes_heterozygous: Option, + /// Maximal number of homozygous carriers in gnomAD exomes. + pub gnomad_exomes_homozygous: Option, + /// Maximal number of hemizygous carriers in gnomAD exomes. + pub gnomad_exomes_hemizygous: Option, + + /// Maximal frequency in gnomAD genomes. + pub gnomad_genomes_frequency: Option, + /// Maximal number of heterozygous carriers in gnomAD genomes. + pub gnomad_genomes_heterozygous: Option, + /// Maximal number of homozygous carriers in gnomAD genomes. + pub gnomad_genomes_homozygous: Option, + /// Maximal number of hemizygous carriers in gnomAD genomes. + pub gnomad_genomes_hemizygous: Option, + + /// Maximal number of in-house carriers. + pub inhouse_carriers: Option, + /// Maximal number of in-house heterozygous carriers. + pub inhouse_heterozygous: Option, + /// Maximal number of in-house homozygous carriers. + pub inhouse_homozygous: Option, + /// Maximal number of in-house hemizygous carriers. + pub inhouse_hemizygous: Option, + + /// Maximal frequency in HelixMtDb + pub helixmtdb_frequency: Option, + /// Maximal number of heterozygous carriers in HelixMtDb. + pub helixmtdb_heteroplasmic: Option, + /// Maximal number of homozygous carriers in HelixMtDb. + pub helixmtdb_homoplasmic: Option, +} + +impl Default for CaseQuery { + /// Returns default values for a `CaseQuery` which makes all variants pass. + fn default() -> Self { + Self { + consequences: mehari::annotate::seqvars::ann::Consequence::all(), + gnomad_exomes_enabled: Default::default(), + gnomad_genomes_enabled: Default::default(), + inhouse_enabled: Default::default(), + helixmtdb_enabled: Default::default(), + quality: Default::default(), + genotype: Default::default(), + transcripts_coding: true, + transcripts_noncoding: true, + var_type_snv: true, + var_type_indel: true, + var_type_mnv: true, + max_exon_dist: Default::default(), + gene_allowlist: Default::default(), + genomic_regions: Default::default(), + require_in_clinvar: Default::default(), + clinvar_include_benign: true, + clinvar_include_pathogenic: true, + clinvar_include_likely_benign: true, + clinvar_include_likely_pathogenic: true, + clinvar_include_uncertain_significance: true, + gnomad_exomes_frequency: Default::default(), + gnomad_exomes_heterozygous: Default::default(), + gnomad_exomes_homozygous: Default::default(), + gnomad_exomes_hemizygous: Default::default(), + gnomad_genomes_frequency: Default::default(), + gnomad_genomes_heterozygous: Default::default(), + gnomad_genomes_homozygous: Default::default(), + gnomad_genomes_hemizygous: Default::default(), + inhouse_carriers: Default::default(), + inhouse_heterozygous: Default::default(), + inhouse_homozygous: Default::default(), + inhouse_hemizygous: Default::default(), + helixmtdb_frequency: Default::default(), + helixmtdb_heteroplasmic: Default::default(), + helixmtdb_homoplasmic: Default::default(), + } + } +} + +impl CaseQuery { + /// Return whether recessive mode has been enabled. + pub fn recessive_mode(&self) -> bool { + self.genotype.values().any(|gt_choice| { + matches!( + gt_choice, + Some(GenotypeChoice::ComphetIndex) + | Some(GenotypeChoice::RecessiveIndex) + | Some(GenotypeChoice::RecessiveParent) + ) + }) + } + + /// Returns name of the recessive index sample. + pub fn index_sample(&self) -> Option { + self.genotype + .iter() + .find_map(|(name, gt_choice)| match gt_choice { + Some(GenotypeChoice::ComphetIndex) | Some(GenotypeChoice::RecessiveIndex) => { + Some(name.clone()) + } + _ => None, + }) + } +} +/// Information on the call as written out by ingest. +/// +/// Note that the ingested files have exactly one alternate allele. +#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)] +pub struct CallInfo { + /// The genotype, if applicable, e.g., "0/1" + pub genotype: Option, + /// Genotype quality score, if applicable + pub quality: Option, + /// Total read coverage at site in the sample. + pub dp: Option, + /// Alternate allele depth for the single allele in the sample. + pub ad: Option, + /// Physical phasing ID for this sample. + pub phasing_id: Option, +} + +/// Definition of a sequence variant with per-sample genotype calls. +/// +/// This uses a subset/specialization of what is described by the VCF standard +/// for the purpose of running SV queries in `varfish-server-worker`. +#[derive(serde::Serialize, serde::Deserialize, PartialEq, Debug, Clone, Default)] +pub struct SequenceVariant { + /// Chromosome name + pub chrom: String, + /// 1-based start position of the variant (or position on first chromosome + /// for break-ends) + pub pos: i32, + /// Reference allele. + pub reference: String, + /// Alternative allele. + pub alternative: String, + + /// Variant effect annotation. + pub ann_fields: Vec, + + /// Number of alleles in gnomAD exomes (not for chrMT). + pub gnomad_exomes_an: i32, + /// Number of homozygous carriers in gnomAD exomes (not for chrMT). + pub gnomad_exomes_hom: i32, + /// Number of heterozygous carriers in gnomAD exomes (not for chrMT). + pub gnomad_exomes_het: i32, + /// Number of hemizygous carriers in gnomAD exomes (not for chrMT). + pub gnomad_exomes_hemi: i32, + + /// Number of alleles in gnomAD genomes (also for chrMT). + pub gnomad_genomes_an: i32, + /// Number of homozygous carriers in gnomAD genomes (also for chrMT). + pub gnomad_genomes_hom: i32, + /// Number of heterozygous carriers in gnomAD genomes (also for chrMT). + pub gnomad_genomes_het: i32, + /// Number of hemizygous carriers in gnomAD genomes (not for chrMT). + pub gnomad_genomes_hemi: i32, + + /// Number of alleles in HelixMtDb cohort (only chrMT). + pub helix_an: i32, + /// Number of homoplasmic carriers in HelixMtDb cohort (only chrMT). + pub helix_hom: i32, + /// Number of heteroplasmic carriers in HelixMtDb cohort (only chrMT). + pub helix_het: i32, + + /// Number of in-house alleles (also for chrMT). + pub inhouse_an: i32, + /// Number of homozygous carriers in in-house cohort (also for chrMT). + pub inhouse_hom: i32, + /// Number of heterozygous carriers in in-house cohort (also for chrMT). + pub inhouse_het: i32, + /// Number of hemizygous carriers in in-house cohort (not for chrMT). + pub inhouse_hemi: i32, + + /// Mapping of sample to genotype information for the SV. + pub call_info: indexmap::IndexMap, +} + +impl SequenceVariant { + /// Convert from VCF record. + pub fn from_vcf(record: &vcf::Record, header: &vcf::Header) -> Result { + let chrom = record.chromosome().to_string(); + let pos: usize = record.position().into(); + let pos = pos as i32; + + let reference = record.reference_bases().to_string(); + let alternative = record.alternate_bases()[0].to_string(); + + let call_info = Self::build_call_info(record, header)?; + let ann_fields = Self::extract_ann_fields(record)?; + + let result = Self { + chrom, + pos, + reference, + alternative, + call_info, + ann_fields, + ..Default::default() + }; + + Self::with_freqs(result, record) + } + + /// Build call information. + fn build_call_info( + record: &vcf::Record, + header: &vcf::Header, + ) -> Result, anyhow::Error> { + let mut result = indexmap::IndexMap::new(); + + for (name, sample) in header + .sample_names() + .iter() + .zip(record.genotypes().values()) + { + let genotype = if let Some(Some(vcf::record::genotypes::sample::Value::String(gt))) = + sample.get(&vcf::record::genotypes::keys::key::GENOTYPE) + { + Some(gt.clone()) + } else { + None + }; + let quality = + if let Some(Some(vcf::record::genotypes::sample::Value::Integer(quality))) = + sample.get(&vcf::record::genotypes::keys::key::CONDITIONAL_GENOTYPE_QUALITY) + { + Some(*quality as f32) + } else { + None + }; + let dp = if let Some(Some(vcf::record::genotypes::sample::Value::Integer(dp))) = + sample.get(&vcf::record::genotypes::keys::key::READ_DEPTH) + { + Some(*dp) + } else { + None + }; + let ad = if let Some(Some(vcf::record::genotypes::sample::Value::Array( + vcf::record::genotypes::sample::value::Array::Integer(ad), + ))) = sample.get(&vcf::record::genotypes::keys::key::READ_DEPTHS) + { + Some(ad[1].expect("empty AD?")) + } else { + None + }; + let phase_set = if let Some(Some(vcf::record::genotypes::sample::Value::Integer(id))) = + sample.get(&vcf::record::genotypes::keys::key::PHASE_SET) + { + Some(*id) + } else { + None + }; + + result.insert( + name.clone(), + CallInfo { + genotype, + quality, + dp, + ad, + phasing_id: phase_set, + }, + ); + } + + Ok(result) + } + + /// Extract `INFO/ANN` entries + fn extract_ann_fields( + record: &vcf::Record, + ) -> Result, anyhow::Error> { + if let Some(Some(ann)) = record.info().get( + &"ANN" + .parse::() + .expect("invalid key INFO/ANN?"), + ) { + if let vcf::record::info::field::Value::Array( + vcf::record::info::field::value::Array::String(ann), + ) = ann + { + ann.iter() + .flatten() + .map(|s| s.parse::()) + .collect::, _>>() + .map_err(|e| anyhow::anyhow!("problem parsing ANN: {}", e)) + } else { + anyhow::bail!("invalid type of INFO/ANN") + } + } else { + Ok(Vec::default()) + } + } + + /// Copy the frequencies from `record` to `result`. + fn with_freqs( + result: SequenceVariant, + record: &vcf::Record, + ) -> Result { + use vcf::record::info::field::Key; + use vcf::record::info::field::Value; + + macro_rules! extract_key { + ($key:ident) => { + let $key = if let Some(Some(Value::Integer($key))) = record.info().get( + &stringify!($key) + .parse::() + .expect(&format!("could not parse key: {:?}", stringify!($key))), + ) { + *$key + } else { + 0 + }; + }; + } + + extract_key!(gnomad_exomes_an); + extract_key!(gnomad_exomes_hom); + extract_key!(gnomad_exomes_het); + extract_key!(gnomad_exomes_hemi); + + extract_key!(gnomad_genomes_an); + extract_key!(gnomad_genomes_hom); + extract_key!(gnomad_genomes_het); + extract_key!(gnomad_genomes_hemi); + + extract_key!(helix_an); + extract_key!(helix_hom); + extract_key!(helix_het); + + Ok(SequenceVariant { + gnomad_exomes_an, + gnomad_exomes_hom, + gnomad_exomes_het, + gnomad_exomes_hemi, + gnomad_genomes_an, + gnomad_genomes_hom, + gnomad_genomes_het, + gnomad_genomes_hemi, + helix_an, + helix_hom, + helix_het, + ..result + }) + } + + /// Return allele frequency in gnomAD exomes. + pub fn gnomad_exomes_af(&self) -> f32 { + if self.gnomad_exomes_an == 0 { + return 0f32; + } + let an = self.gnomad_exomes_an as f32; + let hom = self.gnomad_exomes_hom as f32; + let het = self.gnomad_exomes_het as f32; + let hemi = self.gnomad_exomes_hemi as f32; + (2.0 * hom + het + hemi) / an + } + + /// Return allele frequency in gnomAD genomes. + pub fn gnomad_genomes_af(&self) -> f32 { + if self.gnomad_genomes_an == 0 { + return 0f32; + } + let an = self.gnomad_genomes_an as f32; + let hom = self.gnomad_genomes_hom as f32; + let het = self.gnomad_genomes_het as f32; + let hemi = self.gnomad_genomes_hemi as f32; + (2.0 * hom + het + hemi) / an + } + + /// Return allele frequency in HelixMtDb. + pub fn helixmtdb_af(&self) -> f32 { + if self.helix_an == 0 { + return 0f32; + } + let an = self.helix_an as f32; + let hom = self.helix_hom as f32; + let het = self.helix_het as f32; + (2.0 * hom + het) / an + } +} + +#[cfg(test)] +pub mod test { + use noodles_vcf as vcf; + use rstest::rstest; + + pub mod genotype_choice { + use super::super::GenotypeChoice::{self, *}; + use rstest::rstest; + + #[rstest] + #[case(Any, &["0", "0/0", "0|0", "1", "1/1", "1|1", "0/1", "0/.", "0|1", "1/0", "1|0", ".", "./.", ".|."], true)] + #[case(Ref, &["0", "0/0", "0|0"], true)] + #[case(Ref, &[ "1", "1/1", "1|1", "0/1", "0/.", "0|1", "1/0", "1|0", ".", "./.", ".|."], false)] + #[case(Het, &["0/1", "0|1", "1/0", "1|0"], true)] + #[case(Het, &["0", "0/0", "0|0", "1", "1/1", "1|1", ".", "./.", ".|."], false)] + #[case(Hom, &["1", "1/1", "1|1"], true)] + #[case(Hom, &["0", "0/0", "0|0", "0/1", "0/.", "0|1", "1/0", "1|0", ".", "./.", ".|."], false)] + #[case(NonHom, &["1", "1/1", "1|1"], false)] + #[case(NonHom, &["0", "0/0", "0|0", "0/1", "0/.", "0|1", "1/0", "1|0", ".", "./.", ".|."], true)] + #[case(Variant, &["1", "1/1", "1|1", "0/1", "0|1", "1/0", "1|0"], true)] + #[case(Variant, &["0", "0/0", "0|0", ".", "./.", ".|."], false)] + pub fn matches( + #[case] genotype_choice: GenotypeChoice, + #[case] gt_strs: &[&str], + #[case] expected: bool, + ) { + for gt_str in gt_strs { + assert_eq!( + genotype_choice.matches(gt_str).unwrap(), + expected, + "{:?} {}", + genotype_choice, + gt_str + ); + } + } + } + + #[rstest] + #[case("tests/seqvars/query/empty.json")] + #[case("tests/seqvars/query/full.json")] + #[case("tests/seqvars/query/with_extra.json")] + pub fn smoke_test_load(#[case] path_input: &str) -> Result<(), anyhow::Error> { + mehari::common::set_snapshot_suffix!("{}", path_input.split('/').last().unwrap()); + + let query: super::CaseQuery = serde_json::from_reader(std::fs::File::open(path_input)?)?; + + insta::assert_yaml_snapshot!(&query); + + Ok(()) + } + + #[rstest::rstest] + #[case("tests/seqvars/query/Case_1.ingested.vcf")] + #[case("tests/seqvars/query/dragen.ingested.vcf")] + pub fn sequence_variant_from_vcf(#[case] path_input: &str) -> Result<(), anyhow::Error> { + mehari::common::set_snapshot_suffix!("{}", path_input.split('/').last().unwrap()); + + let mut vcf_reader = vcf::reader::Builder.build_from_path(path_input).unwrap(); + let header = vcf_reader.read_header()?; + + for record in vcf_reader.records(&header) { + let record = record?; + let seqvar = super::SequenceVariant::from_vcf(&record, &header)?; + + insta::assert_yaml_snapshot!(&seqvar); + } + + Ok(()) + } +} diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-10.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-10.snap new file mode 100644 index 00000000..ea8a551a --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-10.snap @@ -0,0 +1,153 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: "17" +pos: 41273700 +reference: C +alternative: CA +ann_fields: + - allele: + Alt: + alternative: CA + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007294.4 + feature_biotype: Coding + rank: + ord: 2 + total: 22 + hgvs_t: c.80+2333_80+2334insT + hgvs_p: p.? + tx_pos: + ord: 193 + total: 7088 + cds_pos: + ord: 80 + total: 5592 + protein_pos: ~ + distance: 2333 + messages: ~ + - allele: + Alt: + alternative: CA + consequences: + - 5_prime_UTR_variant + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007297.4 + feature_biotype: Coding + rank: + ord: 2 + total: 21 + hgvs_t: c.-8+2333_-8+2334insT + hgvs_p: p.? + tx_pos: + ord: 187 + total: 7028 + cds_pos: + ord: -8 + total: 5451 + protein_pos: ~ + distance: 2333 + messages: ~ + - allele: + Alt: + alternative: CA + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007299.4 + feature_biotype: Coding + rank: + ord: 2 + total: 21 + hgvs_t: c.80+2333_80+2334insT + hgvs_p: p.? + tx_pos: + ord: 187 + total: 3696 + cds_pos: + ord: 80 + total: 2100 + protein_pos: ~ + distance: 2333 + messages: ~ + - allele: + Alt: + alternative: CA + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007300.4 + feature_biotype: Coding + rank: + ord: 2 + total: 23 + hgvs_t: c.80+2333_80+2334insT + hgvs_p: p.? + tx_pos: + ord: 193 + total: 7151 + cds_pos: + ord: 80 + total: 5655 + protein_pos: ~ + distance: 2333 + messages: ~ +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 42 + dp: 14 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/0 + quality: 10 + dp: 7 + ad: 1 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/1 + quality: 65 + dp: 10 + ad: 5 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-11.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-11.snap new file mode 100644 index 00000000..bb20b0c7 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-11.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 73 +reference: A +alternative: G +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 3975 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2871 + ad: 2871 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 3320 + ad: 3320 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-12.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-12.snap new file mode 100644 index 00000000..4663df4f --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-12.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 119 +reference: T +alternative: C +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 5418 + ad: 1 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 4039 + ad: 4039 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 4113 + ad: 4112 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-13.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-13.snap new file mode 100644 index 00000000..f431147a --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-13.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 189 +reference: A +alternative: G +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 3069 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1721 + ad: 1721 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2204 + ad: 2204 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-14.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-14.snap new file mode 100644 index 00000000..af347b0f --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-14.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 195 +reference: T +alternative: C +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2599 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1592 + ad: 1592 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1815 + ad: 1815 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-15.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-15.snap new file mode 100644 index 00000000..33cd6396 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-15.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 204 +reference: T +alternative: C +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2180 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1424 + ad: 1424 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1304 + ad: 1304 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-16.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-16.snap new file mode 100644 index 00000000..142f594b --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-16.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 207 +reference: G +alternative: A +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2115 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1408 + ad: 1408 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1277 + ad: 1277 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-17.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-17.snap new file mode 100644 index 00000000..8f6ebdfd --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-17.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 263 +reference: A +alternative: G +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1288 + ad: 1288 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1204 + ad: 1204 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1031 + ad: 1031 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-18.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-18.snap new file mode 100644 index 00000000..f429c5b7 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-18.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 302 +reference: A +alternative: ACC +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/1 + quality: 99 + dp: 844 + ad: 687 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 1011 + ad: 6 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 803 + ad: 3 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-19.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-19.snap new file mode 100644 index 00000000..55494b5b --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-19.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 310 +reference: T +alternative: TC +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1035 + ad: 1035 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1411 + ad: 1411 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1091 + ad: 1090 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-2.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-2.snap new file mode 100644 index 00000000..156f6013 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-2.snap @@ -0,0 +1,152 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: "17" +pos: 41252332 +reference: T +alternative: C +ann_fields: + - allele: + Alt: + alternative: C + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007294.4 + feature_biotype: Coding + rank: + ord: 6 + total: 22 + hgvs_t: c.442-435A>G + hgvs_p: p.? + tx_pos: + ord: 555 + total: 7088 + cds_pos: + ord: 442 + total: 5592 + protein_pos: ~ + distance: -434 + messages: ~ + - allele: + Alt: + alternative: C + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007297.4 + feature_biotype: Coding + rank: + ord: 5 + total: 21 + hgvs_t: c.301-435A>G + hgvs_p: p.? + tx_pos: + ord: 495 + total: 7028 + cds_pos: + ord: 301 + total: 5451 + protein_pos: ~ + distance: -434 + messages: ~ + - allele: + Alt: + alternative: C + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007299.4 + feature_biotype: Coding + rank: + ord: 6 + total: 21 + hgvs_t: c.442-435A>G + hgvs_p: p.? + tx_pos: + ord: 549 + total: 3696 + cds_pos: + ord: 442 + total: 2100 + protein_pos: ~ + distance: -434 + messages: ~ + - allele: + Alt: + alternative: C + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007300.4 + feature_biotype: Coding + rank: + ord: 6 + total: 23 + hgvs_t: c.442-435A>G + hgvs_p: p.? + tx_pos: + ord: 555 + total: 7151 + cds_pos: + ord: 442 + total: 5655 + protein_pos: ~ + distance: -434 + messages: ~ +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 75 + dp: 25 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/1 + quality: 99 + dp: 28 + ad: 14 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/1 + quality: 99 + dp: 40 + ad: 21 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-20.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-20.snap new file mode 100644 index 00000000..a9d437de --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-20.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 477 +reference: T +alternative: C +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2133 + ad: 2129 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2267 + ad: 1 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 1725 + ad: 0 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-21.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-21.snap new file mode 100644 index 00000000..310a43b6 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-21.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 709 +reference: G +alternative: A +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2494 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2186 + ad: 2186 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1814 + ad: 1813 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-22.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-22.snap new file mode 100644 index 00000000..11eb67dc --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-22.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 750 +reference: A +alternative: G +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2757 + ad: 2757 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2392 + ad: 2392 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1621 + ad: 1621 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-23.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-23.snap new file mode 100644 index 00000000..52e88480 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-23.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 879 +reference: T +alternative: C +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2853 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2784 + ad: 0 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/1 + quality: 99 + dp: 1898 + ad: 547 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-24.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-24.snap new file mode 100644 index 00000000..d02d8910 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-24.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 1243 +reference: T +alternative: C +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2675 + ad: 1 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2198 + ad: 2198 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1655 + ad: 1655 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-25.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-25.snap new file mode 100644 index 00000000..889e4c1c --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-25.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 1438 +reference: A +alternative: G +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 3815 + ad: 3815 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 3653 + ad: 3653 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2900 + ad: 2900 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-26.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-26.snap new file mode 100644 index 00000000..2565a6d2 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-26.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 1824 +reference: T +alternative: C +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2668 + ad: 2668 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2409 + ad: 0 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 1752 + ad: 0 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-27.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-27.snap new file mode 100644 index 00000000..2b65e782 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-27.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 2633 +reference: A +alternative: G +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2535 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/1 + quality: 99 + dp: 2409 + ad: 761 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2269 + ad: 0 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-28.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-28.snap new file mode 100644 index 00000000..57c7e49f --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-28.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 2706 +reference: A +alternative: G +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 3200 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2847 + ad: 2847 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2020 + ad: 2020 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-29.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-29.snap new file mode 100644 index 00000000..cf412727 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-29.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 3010 +reference: G +alternative: A +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2841 + ad: 2841 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2385 + ad: 0 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 1685 + ad: 0 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-3.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-3.snap new file mode 100644 index 00000000..fcd8fe39 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-3.snap @@ -0,0 +1,152 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: "17" +pos: 41252691 +reference: ATATAAT +alternative: A +ann_fields: + - allele: + Alt: + alternative: A + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007294.4 + feature_biotype: Coding + rank: + ord: 6 + total: 22 + hgvs_t: c.442-800_442-795delATTATA + hgvs_p: p.? + tx_pos: + ord: 555 + total: 7088 + cds_pos: + ord: 442 + total: 5592 + protein_pos: ~ + distance: -794 + messages: ~ + - allele: + Alt: + alternative: A + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007297.4 + feature_biotype: Coding + rank: + ord: 5 + total: 21 + hgvs_t: c.301-800_301-795delATTATA + hgvs_p: p.? + tx_pos: + ord: 495 + total: 7028 + cds_pos: + ord: 301 + total: 5451 + protein_pos: ~ + distance: -794 + messages: ~ + - allele: + Alt: + alternative: A + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007299.4 + feature_biotype: Coding + rank: + ord: 6 + total: 21 + hgvs_t: c.442-800_442-795delATTATA + hgvs_p: p.? + tx_pos: + ord: 549 + total: 3696 + cds_pos: + ord: 442 + total: 2100 + protein_pos: ~ + distance: -794 + messages: ~ + - allele: + Alt: + alternative: A + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007300.4 + feature_biotype: Coding + rank: + ord: 6 + total: 23 + hgvs_t: c.442-800_442-795delATTATA + hgvs_p: p.? + tx_pos: + ord: 555 + total: 7151 + cds_pos: + ord: 442 + total: 5655 + protein_pos: ~ + distance: -794 + messages: ~ +gnomad_exomes_an: 2368 +gnomad_exomes_hom: 10 +gnomad_exomes_het: 80 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 27 + dp: 9 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/1 + quality: 99 + dp: 14 + ad: 10 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/1 + quality: 99 + dp: 23 + ad: 11 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-30.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-30.snap new file mode 100644 index 00000000..307066a9 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-30.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 3505 +reference: A +alternative: G +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2594 + ad: 14 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2363 + ad: 2363 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1664 + ad: 1664 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-31.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-31.snap new file mode 100644 index 00000000..2529f4a5 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-31.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 3784 +reference: T +alternative: C +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/1 + quality: 99 + dp: 2936 + ad: 2456 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2504 + ad: 0 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 1991 + ad: 0 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-32.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-32.snap new file mode 100644 index 00000000..d6b2b453 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-32.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 4769 +reference: A +alternative: G +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2689 + ad: 2689 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2549 + ad: 2549 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2108 + ad: 2108 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-33.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-33.snap new file mode 100644 index 00000000..831dd047 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-33.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 5046 +reference: G +alternative: A +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2878 + ad: 2 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2466 + ad: 2466 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1661 + ad: 1661 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-34.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-34.snap new file mode 100644 index 00000000..4de50be9 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-34.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 5460 +reference: G +alternative: A +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2907 + ad: 2 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2759 + ad: 2759 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1970 + ad: 1968 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-35.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-35.snap new file mode 100644 index 00000000..523e380f --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-35.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 7028 +reference: C +alternative: T +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2580 + ad: 3 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2203 + ad: 2201 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1946 + ad: 1945 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-36.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-36.snap new file mode 100644 index 00000000..648b8eb2 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-36.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 7864 +reference: C +alternative: T +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 3589 + ad: 1 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 3465 + ad: 3465 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2746 + ad: 2746 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-37.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-37.snap new file mode 100644 index 00000000..c9ced7c0 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-37.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 8170 +reference: A +alternative: G +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2052 + ad: 1 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2257 + ad: 2257 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1774 + ad: 1774 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-38.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-38.snap new file mode 100644 index 00000000..5760a179 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-38.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 8251 +reference: G +alternative: A +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2360 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2317 + ad: 2317 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1625 + ad: 1624 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-39.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-39.snap new file mode 100644 index 00000000..ec318992 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-39.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 8860 +reference: A +alternative: G +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 3278 + ad: 3278 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 3088 + ad: 3088 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2241 + ad: 2241 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-4.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-4.snap new file mode 100644 index 00000000..f7bd9e44 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-4.snap @@ -0,0 +1,152 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: "17" +pos: 41252693 +reference: ATAAT +alternative: A +ann_fields: + - allele: + Alt: + alternative: A + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007294.4 + feature_biotype: Coding + rank: + ord: 6 + total: 22 + hgvs_t: c.442-800_442-797delATTA + hgvs_p: p.? + tx_pos: + ord: 555 + total: 7088 + cds_pos: + ord: 442 + total: 5592 + protein_pos: ~ + distance: -796 + messages: ~ + - allele: + Alt: + alternative: A + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007297.4 + feature_biotype: Coding + rank: + ord: 5 + total: 21 + hgvs_t: c.301-800_301-797delATTA + hgvs_p: p.? + tx_pos: + ord: 495 + total: 7028 + cds_pos: + ord: 301 + total: 5451 + protein_pos: ~ + distance: -796 + messages: ~ + - allele: + Alt: + alternative: A + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007299.4 + feature_biotype: Coding + rank: + ord: 6 + total: 21 + hgvs_t: c.442-800_442-797delATTA + hgvs_p: p.? + tx_pos: + ord: 549 + total: 3696 + cds_pos: + ord: 442 + total: 2100 + protein_pos: ~ + distance: -796 + messages: ~ + - allele: + Alt: + alternative: A + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007300.4 + feature_biotype: Coding + rank: + ord: 6 + total: 23 + hgvs_t: c.442-800_442-797delATTA + hgvs_p: p.? + tx_pos: + ord: 555 + total: 7151 + cds_pos: + ord: 442 + total: 5655 + protein_pos: ~ + distance: -796 + messages: ~ +gnomad_exomes_an: 3866 +gnomad_exomes_hom: 244 +gnomad_exomes_het: 618 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 27 + dp: 9 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/0 + quality: 42 + dp: 14 + ad: 0 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/1 + quality: 99 + dp: 22 + ad: 11 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-40.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-40.snap new file mode 100644 index 00000000..f8af2345 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-40.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 8994 +reference: G +alternative: A +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2793 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2368 + ad: 2368 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1918 + ad: 1917 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-41.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-41.snap new file mode 100644 index 00000000..c516bb7b --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-41.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 9007 +reference: A +alternative: G +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2959 + ad: 2959 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2442 + ad: 0 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 1735 + ad: 0 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-42.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-42.snap new file mode 100644 index 00000000..3a947c58 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-42.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 9150 +reference: A +alternative: G +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 3163 + ad: 3163 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 3538 + ad: 0 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2767 + ad: 0 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-43.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-43.snap new file mode 100644 index 00000000..b6ee84c9 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-43.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 9380 +reference: G +alternative: A +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 3321 + ad: 3320 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 3222 + ad: 0 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2547 + ad: 0 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-44.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-44.snap new file mode 100644 index 00000000..5b3965a6 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-44.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 10097 +reference: A +alternative: G +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2660 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/1 + quality: 99 + dp: 2188 + ad: 508 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 1851 + ad: 0 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-45.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-45.snap new file mode 100644 index 00000000..d7a3d490 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-45.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 11204 +reference: T +alternative: C +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 3173 + ad: 5 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2922 + ad: 2922 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2418 + ad: 2418 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-46.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-46.snap new file mode 100644 index 00000000..f752c0c4 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-46.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 11674 +reference: C +alternative: T +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2890 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2666 + ad: 2666 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2180 + ad: 2179 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-47.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-47.snap new file mode 100644 index 00000000..a908c454 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-47.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 11719 +reference: G +alternative: A +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 3341 + ad: 2 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 3052 + ad: 3052 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2203 + ad: 2203 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-48.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-48.snap new file mode 100644 index 00000000..4230ce2e --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-48.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 11947 +reference: A +alternative: G +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2581 + ad: 2 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2273 + ad: 2273 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1804 + ad: 1804 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-49.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-49.snap new file mode 100644 index 00000000..f6dbe51e --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-49.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 12414 +reference: T +alternative: C +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2855 + ad: 3 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2546 + ad: 2545 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1733 + ad: 1733 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-5.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-5.snap new file mode 100644 index 00000000..d4dc9781 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-5.snap @@ -0,0 +1,152 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: "17" +pos: 41252695 +reference: AAT +alternative: A +ann_fields: + - allele: + Alt: + alternative: A + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007294.4 + feature_biotype: Coding + rank: + ord: 6 + total: 22 + hgvs_t: c.442-800_442-799delAT + hgvs_p: p.? + tx_pos: + ord: 555 + total: 7088 + cds_pos: + ord: 442 + total: 5592 + protein_pos: ~ + distance: -798 + messages: ~ + - allele: + Alt: + alternative: A + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007297.4 + feature_biotype: Coding + rank: + ord: 5 + total: 21 + hgvs_t: c.301-800_301-799delAT + hgvs_p: p.? + tx_pos: + ord: 495 + total: 7028 + cds_pos: + ord: 301 + total: 5451 + protein_pos: ~ + distance: -798 + messages: ~ + - allele: + Alt: + alternative: A + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007299.4 + feature_biotype: Coding + rank: + ord: 6 + total: 21 + hgvs_t: c.442-800_442-799delAT + hgvs_p: p.? + tx_pos: + ord: 549 + total: 3696 + cds_pos: + ord: 442 + total: 2100 + protein_pos: ~ + distance: -798 + messages: ~ + - allele: + Alt: + alternative: A + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007300.4 + feature_biotype: Coding + rank: + ord: 6 + total: 23 + hgvs_t: c.442-800_442-799delAT + hgvs_p: p.? + tx_pos: + ord: 555 + total: 7151 + cds_pos: + ord: 442 + total: 5655 + protein_pos: ~ + distance: -798 + messages: ~ +gnomad_exomes_an: 5066 +gnomad_exomes_hom: 546 +gnomad_exomes_het: 795 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/1 + quality: 79 + dp: 9 + ad: 6 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/0 + quality: 42 + dp: 14 + ad: 0 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/0 + quality: 66 + dp: 22 + ad: 0 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-50.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-50.snap new file mode 100644 index 00000000..1c4be3ce --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-50.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 12648 +reference: A +alternative: G +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 1813 + ad: 1 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1664 + ad: 1662 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1781 + ad: 1777 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-51.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-51.snap new file mode 100644 index 00000000..a3fb78f1 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-51.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 12705 +reference: C +alternative: T +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2369 + ad: 10 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2138 + ad: 2137 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1622 + ad: 1621 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-52.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-52.snap new file mode 100644 index 00000000..65aee969 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-52.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 13406 +reference: G +alternative: A +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2540 + ad: 1 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2216 + ad: 0 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/1 + quality: 99 + dp: 1957 + ad: 733 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-53.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-53.snap new file mode 100644 index 00000000..50a65e0f --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-53.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 13611 +reference: A +alternative: G +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 3840 + ad: 2 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 3717 + ad: 3717 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2835 + ad: 2834 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-54.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-54.snap new file mode 100644 index 00000000..5aae45c8 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-54.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 13928 +reference: G +alternative: C +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 2947 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2700 + ad: 2700 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1880 + ad: 1880 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-55.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-55.snap new file mode 100644 index 00000000..67f9dfb2 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-55.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 14148 +reference: A +alternative: G +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 3021 + ad: 2 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2820 + ad: 2820 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1962 + ad: 1962 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-56.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-56.snap new file mode 100644 index 00000000..e5034b92 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-56.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 14766 +reference: C +alternative: T +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 3321 + ad: 3 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 3113 + ad: 3111 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2358 + ad: 2355 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-57.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-57.snap new file mode 100644 index 00000000..40e96f9a --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-57.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 15326 +reference: A +alternative: G +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 3716 + ad: 3716 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 3560 + ad: 3560 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2690 + ad: 2690 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-58.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-58.snap new file mode 100644 index 00000000..da93858a --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-58.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 15884 +reference: G +alternative: C +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 3596 + ad: 1 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 3167 + ad: 3167 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2734 + ad: 2733 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-59.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-59.snap new file mode 100644 index 00000000..3f6ee55a --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-59.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 16184 +reference: C +alternative: T +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 1407 + ad: 1 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1969 + ad: 1969 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1478 + ad: 1478 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-6.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-6.snap new file mode 100644 index 00000000..da1d0b9b --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-6.snap @@ -0,0 +1,152 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: "17" +pos: 41252696 +reference: A +alternative: T +ann_fields: + - allele: + Alt: + alternative: T + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007294.4 + feature_biotype: Coding + rank: + ord: 6 + total: 22 + hgvs_t: c.442-799T>A + hgvs_p: p.? + tx_pos: + ord: 555 + total: 7088 + cds_pos: + ord: 442 + total: 5592 + protein_pos: ~ + distance: -798 + messages: ~ + - allele: + Alt: + alternative: T + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007297.4 + feature_biotype: Coding + rank: + ord: 5 + total: 21 + hgvs_t: c.301-799T>A + hgvs_p: p.? + tx_pos: + ord: 495 + total: 7028 + cds_pos: + ord: 301 + total: 5451 + protein_pos: ~ + distance: -798 + messages: ~ + - allele: + Alt: + alternative: T + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007299.4 + feature_biotype: Coding + rank: + ord: 6 + total: 21 + hgvs_t: c.442-799T>A + hgvs_p: p.? + tx_pos: + ord: 549 + total: 3696 + cds_pos: + ord: 442 + total: 2100 + protein_pos: ~ + distance: -798 + messages: ~ + - allele: + Alt: + alternative: T + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007300.4 + feature_biotype: Coding + rank: + ord: 6 + total: 23 + hgvs_t: c.442-799T>A + hgvs_p: p.? + tx_pos: + ord: 555 + total: 7151 + cds_pos: + ord: 442 + total: 5655 + protein_pos: ~ + distance: -798 + messages: ~ +gnomad_exomes_an: 4200 +gnomad_exomes_hom: 29 +gnomad_exomes_het: 334 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/1 + quality: 78 + dp: 9 + ad: 3 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/1 + quality: 98 + dp: 14 + ad: 4 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/0 + quality: 67 + dp: 22 + ad: 0 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-60.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-60.snap new file mode 100644 index 00000000..733bc601 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-60.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 16223 +reference: C +alternative: T +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 1406 + ad: 1 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 2018 + ad: 2018 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1472 + ad: 1472 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-61.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-61.snap new file mode 100644 index 00000000..8e83474f --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-61.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 16263 +reference: T +alternative: C +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1478 + ad: 1476 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 1994 + ad: 0 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 1475 + ad: 0 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-62.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-62.snap new file mode 100644 index 00000000..dc5dd74e --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-62.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 16292 +reference: C +alternative: T +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 1652 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1914 + ad: 1913 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1476 + ad: 1476 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-63.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-63.snap new file mode 100644 index 00000000..d27eab90 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-63.snap @@ -0,0 +1,44 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 16519 +reference: T +alternative: C +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1759 + ad: 1759 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 4094 + ad: 4094 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 1744 + ad: 1744 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-7.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-7.snap new file mode 100644 index 00000000..32f1cc4d --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-7.snap @@ -0,0 +1,152 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: "17" +pos: 41252697 +reference: A +alternative: AT +ann_fields: + - allele: + Alt: + alternative: AT + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007294.4 + feature_biotype: Coding + rank: + ord: 6 + total: 22 + hgvs_t: c.442-801_442-800insA + hgvs_p: p.? + tx_pos: + ord: 555 + total: 7088 + cds_pos: + ord: 442 + total: 5592 + protein_pos: ~ + distance: -800 + messages: ~ + - allele: + Alt: + alternative: AT + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007297.4 + feature_biotype: Coding + rank: + ord: 5 + total: 21 + hgvs_t: c.301-801_301-800insA + hgvs_p: p.? + tx_pos: + ord: 495 + total: 7028 + cds_pos: + ord: 301 + total: 5451 + protein_pos: ~ + distance: -800 + messages: ~ + - allele: + Alt: + alternative: AT + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007299.4 + feature_biotype: Coding + rank: + ord: 6 + total: 21 + hgvs_t: c.442-801_442-800insA + hgvs_p: p.? + tx_pos: + ord: 549 + total: 3696 + cds_pos: + ord: 442 + total: 2100 + protein_pos: ~ + distance: -800 + messages: ~ + - allele: + Alt: + alternative: AT + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007300.4 + feature_biotype: Coding + rank: + ord: 6 + total: 23 + hgvs_t: c.442-801_442-800insA + hgvs_p: p.? + tx_pos: + ord: 555 + total: 7151 + cds_pos: + ord: 442 + total: 5655 + protein_pos: ~ + distance: -800 + messages: ~ +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 1/1 + quality: 99 + dp: 45 + ad: 45 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 1/0 + quality: 99 + dp: 33 + ad: 17 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 1/0 + quality: 99 + dp: 33 + ad: 11 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-8.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-8.snap new file mode 100644 index 00000000..1ab2b11d --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-8.snap @@ -0,0 +1,152 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: "17" +pos: 41252697 +reference: A +alternative: ATT +ann_fields: + - allele: + Alt: + alternative: ATT + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007294.4 + feature_biotype: Coding + rank: + ord: 6 + total: 22 + hgvs_t: c.442-801_442-800insAA + hgvs_p: p.? + tx_pos: + ord: 555 + total: 7088 + cds_pos: + ord: 442 + total: 5592 + protein_pos: ~ + distance: -800 + messages: ~ + - allele: + Alt: + alternative: ATT + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007297.4 + feature_biotype: Coding + rank: + ord: 5 + total: 21 + hgvs_t: c.301-801_301-800insAA + hgvs_p: p.? + tx_pos: + ord: 495 + total: 7028 + cds_pos: + ord: 301 + total: 5451 + protein_pos: ~ + distance: -800 + messages: ~ + - allele: + Alt: + alternative: ATT + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007299.4 + feature_biotype: Coding + rank: + ord: 6 + total: 21 + hgvs_t: c.442-801_442-800insAA + hgvs_p: p.? + tx_pos: + ord: 549 + total: 3696 + cds_pos: + ord: 442 + total: 2100 + protein_pos: ~ + distance: -800 + messages: ~ + - allele: + Alt: + alternative: ATT + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007300.4 + feature_biotype: Coding + rank: + ord: 6 + total: 23 + hgvs_t: c.442-801_442-800insAA + hgvs_p: p.? + tx_pos: + ord: 555 + total: 7151 + cds_pos: + ord: 442 + total: 5655 + protein_pos: ~ + distance: -800 + messages: ~ +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 45 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/1 + quality: 99 + dp: 33 + ad: 16 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/1 + quality: 99 + dp: 33 + ad: 21 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-9.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-9.snap new file mode 100644 index 00000000..263611dd --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf-9.snap @@ -0,0 +1,152 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: "17" +pos: 41254393 +reference: G +alternative: T +ann_fields: + - allele: + Alt: + alternative: T + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007294.4 + feature_biotype: Coding + rank: + ord: 6 + total: 22 + hgvs_t: c.441+1746C>A + hgvs_p: p.? + tx_pos: + ord: 554 + total: 7088 + cds_pos: + ord: 441 + total: 5592 + protein_pos: ~ + distance: 1745 + messages: ~ + - allele: + Alt: + alternative: T + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007297.4 + feature_biotype: Coding + rank: + ord: 5 + total: 21 + hgvs_t: c.300+1746C>A + hgvs_p: p.? + tx_pos: + ord: 494 + total: 7028 + cds_pos: + ord: 300 + total: 5451 + protein_pos: ~ + distance: 1745 + messages: ~ + - allele: + Alt: + alternative: T + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007299.4 + feature_biotype: Coding + rank: + ord: 6 + total: 21 + hgvs_t: c.441+1746C>A + hgvs_p: p.? + tx_pos: + ord: 548 + total: 3696 + cds_pos: + ord: 441 + total: 2100 + protein_pos: ~ + distance: 1745 + messages: ~ + - allele: + Alt: + alternative: T + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007300.4 + feature_biotype: Coding + rank: + ord: 6 + total: 23 + hgvs_t: c.441+1746C>A + hgvs_p: p.? + tx_pos: + ord: 554 + total: 7151 + cds_pos: + ord: 441 + total: 5655 + protein_pos: ~ + distance: 1745 + messages: ~ +gnomad_exomes_an: 1936 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 167 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/1 + quality: 66 + dp: 37 + ad: 8 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: "./." + quality: ~ + dp: ~ + ad: ~ + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/0 + quality: 47 + dp: 35 + ad: 3 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf.snap new file mode 100644 index 00000000..5bd46e2b --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@Case_1.ingested.vcf.snap @@ -0,0 +1,164 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: "17" +pos: 41249263 +reference: G +alternative: A +ann_fields: + - allele: + Alt: + alternative: A + consequences: + - splice_region_variant + - synonymous_variant + putative_impact: MODERATE + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007294.4 + feature_biotype: Coding + rank: + ord: 8 + total: 23 + hgvs_t: c.591C>T + hgvs_p: p.C197= + tx_pos: + ord: 704 + total: 7088 + cds_pos: + ord: 591 + total: 5592 + protein_pos: + ord: 197 + total: 1864 + distance: 44 + messages: ~ + - allele: + Alt: + alternative: A + consequences: + - splice_region_variant + - synonymous_variant + putative_impact: MODERATE + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007297.4 + feature_biotype: Coding + rank: + ord: 7 + total: 22 + hgvs_t: c.450C>T + hgvs_p: p.C150= + tx_pos: + ord: 644 + total: 7028 + cds_pos: + ord: 450 + total: 5451 + protein_pos: + ord: 150 + total: 1817 + distance: 44 + messages: ~ + - allele: + Alt: + alternative: A + consequences: + - splice_region_variant + - synonymous_variant + putative_impact: MODERATE + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007299.4 + feature_biotype: Coding + rank: + ord: 8 + total: 22 + hgvs_t: c.591C>T + hgvs_p: p.C197= + tx_pos: + ord: 698 + total: 3696 + cds_pos: + ord: 591 + total: 2100 + protein_pos: + ord: 197 + total: 700 + distance: 44 + messages: ~ + - allele: + Alt: + alternative: A + consequences: + - splice_region_variant + - synonymous_variant + putative_impact: MODERATE + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007300.4 + feature_biotype: Coding + rank: + ord: 8 + total: 24 + hgvs_t: c.591C>T + hgvs_p: p.C197= + tx_pos: + ord: 704 + total: 7151 + cds_pos: + ord: 591 + total: 5655 + protein_pos: + ord: 197 + total: 1885 + distance: 44 + messages: ~ +gnomad_exomes_an: 31398 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 56 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 251304 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 369 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + Case_1_father-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 52 + ad: 0 + phasing_id: ~ + Case_1_index-N1-DNA1-WGS1: + genotype: 0/0 + quality: 99 + dp: 46 + ad: 0 + phasing_id: ~ + Case_1_mother-N1-DNA1-WGS1: + genotype: 0/1 + quality: 99 + dp: 42 + ad: 21 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@dragen.ingested.vcf-2.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@dragen.ingested.vcf-2.snap new file mode 100644 index 00000000..217c4c06 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@dragen.ingested.vcf-2.snap @@ -0,0 +1,32 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: MT +pos: 750 +reference: A +alternative: G +ann_fields: [] +gnomad_exomes_an: 0 +gnomad_exomes_hom: 0 +gnomad_exomes_het: 0 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + CASE: + genotype: 1/1 + quality: 99 + dp: 35 + ad: 35 + phasing_id: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@dragen.ingested.vcf.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@dragen.ingested.vcf.snap new file mode 100644 index 00000000..8f6575d5 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__sequence_variant_from_vcf@dragen.ingested.vcf.snap @@ -0,0 +1,140 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&seqvar" +--- +chrom: "17" +pos: 41256074 +reference: CA +alternative: C +ann_fields: + - allele: + Alt: + alternative: C + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007294.4 + feature_biotype: Coding + rank: + ord: 6 + total: 22 + hgvs_t: c.441+64delT + hgvs_p: p.? + tx_pos: + ord: 554 + total: 7088 + cds_pos: + ord: 441 + total: 5592 + protein_pos: ~ + distance: 63 + messages: ~ + - allele: + Alt: + alternative: C + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007297.4 + feature_biotype: Coding + rank: + ord: 5 + total: 21 + hgvs_t: c.300+64delT + hgvs_p: p.? + tx_pos: + ord: 494 + total: 7028 + cds_pos: + ord: 300 + total: 5451 + protein_pos: ~ + distance: 63 + messages: ~ + - allele: + Alt: + alternative: C + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007299.4 + feature_biotype: Coding + rank: + ord: 6 + total: 21 + hgvs_t: c.441+64delT + hgvs_p: p.? + tx_pos: + ord: 548 + total: 3696 + cds_pos: + ord: 441 + total: 2100 + protein_pos: ~ + distance: 63 + messages: ~ + - allele: + Alt: + alternative: C + consequences: + - intron_variant + putative_impact: MODIFIER + gene_symbol: BRCA1 + gene_id: "HGNC:1100" + feature_type: + SoTerm: + term: Transcript + feature_id: NM_007300.4 + feature_biotype: Coding + rank: + ord: 6 + total: 23 + hgvs_t: c.441+64delT + hgvs_p: p.? + tx_pos: + ord: 554 + total: 7151 + cds_pos: + ord: 441 + total: 5655 + protein_pos: ~ + distance: 63 + messages: ~ +gnomad_exomes_an: 20150 +gnomad_exomes_hom: 2725 +gnomad_exomes_het: 5476 +gnomad_exomes_hemi: 0 +gnomad_genomes_an: 0 +gnomad_genomes_hom: 0 +gnomad_genomes_het: 0 +gnomad_genomes_hemi: 0 +helix_an: 0 +helix_hom: 0 +helix_het: 0 +inhouse_an: 0 +inhouse_hom: 0 +inhouse_het: 0 +inhouse_hemi: 0 +call_info: + CASE: + genotype: 1|1 + quality: 99 + dp: 80 + ad: 80 + phasing_id: 41256074 + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@empty.json.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@empty.json.snap new file mode 100644 index 00000000..908a0a7f --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@empty.json.snap @@ -0,0 +1,90 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&query" +--- +consequences: + - chromosome_number_variation + - exon_loss_variant + - frameshift_variant + - rare_amino_acid_variant + - splice_acceptor_variant + - splice_donor_variant + - start_lost + - stop_gained + - stop_lost + - transcript_ablation + - 3_prime_UTR_truncation + - 5_prime_UTR_truncation + - conservative_inframe_deletion + - conservative_inframe_insertion + - disruptive_inframe_deletion + - disruptive_inframe_insertion + - missense_variant + - regulatory_region_ablation + - splice_region_variant + - TFBS_ablation + - 5_prime_UTR_premature_start_codon_gain_variant + - initiator_codon_variant + - start_retained + - stop_retained_variant + - synonymous_variant + - 3_prime_UTR_variant + - 5_prime_UTR_variant + - coding_sequence_variant + - conserved_intergenic_variant + - conserved_intron_variant + - downstream_gene_variant + - exon_variant + - feature_elongation + - feature_truncation + - gene_variant + - intergenic_variant + - intron_variant + - mature_miRNA_variant + - miRNA + - NMD_transcript_variant + - non_coding_transcript_exon_variant + - non_coding_transcript_intron_variant + - regulatory_region_amplification + - regulatory_region_variant + - TF_binding_site_variant + - TFBS_amplification + - transcript_amplification + - transcript_variant + - upstream_gene_variant +quality: {} +genotype: {} +transcripts_coding: true +transcripts_noncoding: true +var_type_snv: true +var_type_indel: true +var_type_mnv: true +max_exon_dist: ~ +gene_allowlist: ~ +genomic_regions: ~ +require_in_clinvar: false +clinvar_include_benign: true +clinvar_include_pathogenic: true +clinvar_include_likely_benign: true +clinvar_include_likely_pathogenic: true +clinvar_include_uncertain_significance: true +gnomad_exomes_enabled: false +gnomad_genomes_enabled: false +inhouse_enabled: false +helixmtdb_enabled: false +gnomad_exomes_frequency: ~ +gnomad_exomes_heterozygous: ~ +gnomad_exomes_homozygous: ~ +gnomad_exomes_hemizygous: ~ +gnomad_genomes_frequency: ~ +gnomad_genomes_heterozygous: ~ +gnomad_genomes_homozygous: ~ +gnomad_genomes_hemizygous: ~ +inhouse_carriers: ~ +inhouse_heterozygous: ~ +inhouse_homozygous: ~ +inhouse_hemizygous: ~ +helixmtdb_frequency: ~ +helixmtdb_heteroplasmic: ~ +helixmtdb_homoplasmic: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap new file mode 100644 index 00000000..8b93af25 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@full.json.snap @@ -0,0 +1,99 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&query" +--- +consequences: + - chromosome_number_variation + - exon_loss_variant + - frameshift_variant + - rare_amino_acid_variant + - splice_acceptor_variant + - splice_donor_variant + - start_lost + - stop_gained + - stop_lost + - transcript_ablation + - 3_prime_UTR_truncation + - 5_prime_UTR_truncation + - conservative_inframe_deletion + - conservative_inframe_insertion + - disruptive_inframe_deletion + - disruptive_inframe_insertion + - missense_variant + - regulatory_region_ablation + - splice_region_variant + - TFBS_ablation + - 5_prime_UTR_premature_start_codon_gain_variant + - initiator_codon_variant + - start_retained + - stop_retained_variant + - synonymous_variant + - 3_prime_UTR_variant + - 5_prime_UTR_variant + - coding_sequence_variant + - conserved_intergenic_variant + - conserved_intron_variant + - downstream_gene_variant + - exon_variant + - feature_elongation + - feature_truncation + - gene_variant + - intergenic_variant + - intron_variant + - mature_miRNA_variant + - miRNA + - NMD_transcript_variant + - non_coding_transcript_exon_variant + - non_coding_transcript_intron_variant + - regulatory_region_amplification + - regulatory_region_variant + - TF_binding_site_variant + - TFBS_amplification + - transcript_amplification + - transcript_variant + - upstream_gene_variant +quality: + sample: + dp_het: 10 + dp_hom: 5 + gq: 10 + ab: 0.2 + ad: 3 + ad_max: ~ + fail: drop-variant +genotype: + sample: het +transcripts_coding: true +transcripts_noncoding: true +var_type_snv: true +var_type_indel: true +var_type_mnv: true +max_exon_dist: 100 +gene_allowlist: [] +genomic_regions: ~ +require_in_clinvar: false +clinvar_include_benign: false +clinvar_include_pathogenic: true +clinvar_include_likely_benign: false +clinvar_include_likely_pathogenic: true +clinvar_include_uncertain_significance: false +gnomad_exomes_enabled: true +gnomad_genomes_enabled: true +inhouse_enabled: true +helixmtdb_enabled: true +gnomad_exomes_frequency: 0.002 +gnomad_exomes_heterozygous: 20 +gnomad_exomes_homozygous: 0 +gnomad_exomes_hemizygous: ~ +gnomad_genomes_frequency: 0.002 +gnomad_genomes_heterozygous: 4 +gnomad_genomes_homozygous: 0 +gnomad_genomes_hemizygous: ~ +inhouse_carriers: 20 +inhouse_heterozygous: ~ +inhouse_homozygous: ~ +inhouse_hemizygous: ~ +helixmtdb_frequency: 0.01 +helixmtdb_heteroplasmic: ~ +helixmtdb_homoplasmic: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap new file mode 100644 index 00000000..8b93af25 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__schema__test__smoke_test_load@with_extra.json.snap @@ -0,0 +1,99 @@ +--- +source: src/seqvars/query/schema.rs +expression: "&query" +--- +consequences: + - chromosome_number_variation + - exon_loss_variant + - frameshift_variant + - rare_amino_acid_variant + - splice_acceptor_variant + - splice_donor_variant + - start_lost + - stop_gained + - stop_lost + - transcript_ablation + - 3_prime_UTR_truncation + - 5_prime_UTR_truncation + - conservative_inframe_deletion + - conservative_inframe_insertion + - disruptive_inframe_deletion + - disruptive_inframe_insertion + - missense_variant + - regulatory_region_ablation + - splice_region_variant + - TFBS_ablation + - 5_prime_UTR_premature_start_codon_gain_variant + - initiator_codon_variant + - start_retained + - stop_retained_variant + - synonymous_variant + - 3_prime_UTR_variant + - 5_prime_UTR_variant + - coding_sequence_variant + - conserved_intergenic_variant + - conserved_intron_variant + - downstream_gene_variant + - exon_variant + - feature_elongation + - feature_truncation + - gene_variant + - intergenic_variant + - intron_variant + - mature_miRNA_variant + - miRNA + - NMD_transcript_variant + - non_coding_transcript_exon_variant + - non_coding_transcript_intron_variant + - regulatory_region_amplification + - regulatory_region_variant + - TF_binding_site_variant + - TFBS_amplification + - transcript_amplification + - transcript_variant + - upstream_gene_variant +quality: + sample: + dp_het: 10 + dp_hom: 5 + gq: 10 + ab: 0.2 + ad: 3 + ad_max: ~ + fail: drop-variant +genotype: + sample: het +transcripts_coding: true +transcripts_noncoding: true +var_type_snv: true +var_type_indel: true +var_type_mnv: true +max_exon_dist: 100 +gene_allowlist: [] +genomic_regions: ~ +require_in_clinvar: false +clinvar_include_benign: false +clinvar_include_pathogenic: true +clinvar_include_likely_benign: false +clinvar_include_likely_pathogenic: true +clinvar_include_uncertain_significance: false +gnomad_exomes_enabled: true +gnomad_genomes_enabled: true +inhouse_enabled: true +helixmtdb_enabled: true +gnomad_exomes_frequency: 0.002 +gnomad_exomes_heterozygous: 20 +gnomad_exomes_homozygous: 0 +gnomad_exomes_hemizygous: ~ +gnomad_genomes_frequency: 0.002 +gnomad_genomes_heterozygous: 4 +gnomad_genomes_homozygous: 0 +gnomad_genomes_hemizygous: ~ +inhouse_carriers: 20 +inhouse_heterozygous: ~ +inhouse_homozygous: ~ +inhouse_hemizygous: ~ +helixmtdb_frequency: 0.01 +helixmtdb_heteroplasmic: ~ +helixmtdb_homoplasmic: ~ + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@Case_1.ingested.vcf.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@Case_1.ingested.vcf.snap new file mode 100644 index 00000000..d9dc33d1 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@Case_1.ingested.vcf.snap @@ -0,0 +1,65 @@ +--- +source: src/seqvars/query/mod.rs +expression: "std::fs::read_to_string(args.path_output.as_str())?" +--- +sodar_uuid release chromosome chromosome_no reference alternative bin start end smallvariantqueryresultset_id payload +a2242722-6377-cc86-7d51-ad3f130af08a GRCh37 17 17 G A 899 41249263 41249263 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{"case_uuid":"00000000-0000-0000-0000-000000000000","call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":1652,"ad":0,"gq":99,"gt":"0/0"},"Case_1_index-N1-DNA1-WGS1":{"dp":1914,"ad":1913,"gq":99,"gt":"1/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":1476,"ad":1476,"gq":99,"gt":"1/1"}}}} +bef71ebc-fa2d-758a-cd58-2732175691e4 GRCh37 MT 25 T C 585 16519 16519 . {"case_uuid":"00000000-0000-0000-0000-000000000000","call_related":{"call_info":{"Case_1_father-N1-DNA1-WGS1":{"dp":1759,"ad":1759,"gq":99,"gt":"1/1"},"Case_1_index-N1-DNA1-WGS1":{"dp":4094,"ad":4094,"gq":99,"gt":"1/1"},"Case_1_mother-N1-DNA1-WGS1":{"dp":1744,"ad":1744,"gq":99,"gt":"1/1"}}}} + diff --git a/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@dragen.ingested.vcf.snap b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@dragen.ingested.vcf.snap new file mode 100644 index 00000000..9373a866 --- /dev/null +++ b/src/seqvars/query/snapshots/varfish_server_worker__seqvars__query__test__smoke_test@dragen.ingested.vcf.snap @@ -0,0 +1,8 @@ +--- +source: src/seqvars/query/mod.rs +expression: "std::fs::read_to_string(args.path_output.as_str())?" +--- +sodar_uuid release chromosome chromosome_no reference alternative bin start end smallvariantqueryresultset_id payload +a2242722-6377-cc86-7d51-ad3f130af08a GRCh37 17 17 CA C 899 41256074 41256075 . {"case_uuid":"00000000-0000-0000-0000-000000000000","gene_related":{"identity":{"hgnc_id":"HGNC:1100","hgnc_symbol":"BRCA1"},"consequences":{"hgvs_t":"c.441+64delT","hgvs_p":"p.?","consequences":["intron_variant"]},"phenotype":{"is_acmg_sf":true,"is_disease_gene":true},"constraints":{"gnomad_mis_z":0.58215,"gnomad_oe_lof":0.7311,"gnomad_oe_lof_lower":0.588,"gnomad_oe_lof_upper":0.915,"gnomad_oe_mis":0.9466,"gnomad_oe_mis_lower":0.895,"gnomad_oe_mis_upper":1.0,"gnomad_pli":9.2157e-29,"gnomad_syn_z":0.51097}},"variant_related":{"precomputed_scores":{"PHRED":4.373,"spliceai":0.0,"spliceai_argmax":"SpliceAI-acc-gain"},"db_ids":{"dbsnp_rs":"rs72434991"}},"call_related":{"call_info":{"CASE":{"dp":80,"ad":80,"gq":99,"gt":"1|1"}}}} +d13451de-7160-efa2-b230-76fd782de967 GRCh37 MT 25 A G 585 750 750 . {"case_uuid":"00000000-0000-0000-0000-000000000000","call_related":{"call_info":{"CASE":{"dp":35,"ad":35,"gq":99,"gt":"1/1"}}}} + diff --git a/src/seqvars/query/sorting.rs b/src/seqvars/query/sorting.rs new file mode 100644 index 00000000..b1795c23 --- /dev/null +++ b/src/seqvars/query/sorting.rs @@ -0,0 +1,79 @@ +//! Code for sorting `SequenceVariant` records by HGNC ID or coordinate. + +use super::schema::SequenceVariant; + +/// Helper wrapper that allows to sort `SequenceVariant` by HGNC ID. +#[derive(Debug, serde::Serialize, serde::Deserialize)] +pub struct ByHgncId { + pub hgnc_id: String, + pub seqvar: SequenceVariant, +} + +impl From for ByHgncId { + fn from(val: SequenceVariant) -> Self { + Self { + hgnc_id: if !val.ann_fields.is_empty() { + val.ann_fields[0].gene_id.clone() + } else { + String::new() + }, + seqvar: val, + } + } +} + +impl PartialEq for ByHgncId { + fn eq(&self, other: &Self) -> bool { + self.hgnc_id == other.hgnc_id + } +} + +impl Eq for ByHgncId {} + +impl PartialOrd for ByHgncId { + fn partial_cmp(&self, other: &Self) -> Option { + Some(self.cmp(other)) + } +} + +impl Ord for ByHgncId { + fn cmp(&self, other: &Self) -> std::cmp::Ordering { + self.hgnc_id.cmp(&other.hgnc_id) + } +} + +/// Helper wrapper that allows to sort `SequenceVariant` by coordinate. +#[derive(Debug, serde::Serialize, serde::Deserialize)] +pub struct ByCoordinate { + pub coordinate: (String, i32), + pub seqvar: SequenceVariant, +} + +impl From for ByCoordinate { + fn from(val: SequenceVariant) -> Self { + Self { + coordinate: (val.chrom.clone(), val.pos), + seqvar: val, + } + } +} + +impl PartialEq for ByCoordinate { + fn eq(&self, other: &Self) -> bool { + self.coordinate == other.coordinate + } +} + +impl Eq for ByCoordinate {} + +impl PartialOrd for ByCoordinate { + fn partial_cmp(&self, other: &Self) -> Option { + Some(self.cmp(other)) + } +} + +impl Ord for ByCoordinate { + fn cmp(&self, other: &Self) -> std::cmp::Ordering { + self.coordinate.cmp(&other.coordinate) + } +} diff --git a/src/strucvars/aggregate/cli.rs b/src/strucvars/aggregate/cli.rs index cf6f331a..16034c25 100644 --- a/src/strucvars/aggregate/cli.rs +++ b/src/strucvars/aggregate/cli.rs @@ -3,7 +3,7 @@ use std::{ collections::HashMap, fs::File, - io::{BufReader, BufWriter, Write}, + io::{BufRead, BufReader, BufWriter, Write}, path::{Path, PathBuf}, time::Instant, }; @@ -13,7 +13,6 @@ use clap::{command, Parser}; use mehari::common::open_read_maybe_gz; use noodles_vcf as vcf; use serde_json::to_writer; -use serde_jsonlines::JsonLinesReader; use strum::IntoEnumIterator; use thousands::Separable; @@ -130,8 +129,20 @@ fn merge_to_out( let mut records: Vec = Vec::new(); // Read in all records and perform the "merge compression" - let mut reader = JsonLinesReader::new(reader); - while let Ok(Some(record)) = reader.read::() { + for line in reader.lines() { + let line = if let Ok(line) = line { + line + } else { + anyhow::bail!("error reading line from input file") + }; + let record: super::output::Record = serde_json::from_str(&line).map_err(|e| { + anyhow::anyhow!( + "error parsing line from input file: {:?} (line: {:?})", + e, + &line + ) + })?; + let begin = match record.sv_type { SvType::Bnd => record.begin - 1 - args.slack_bnd, SvType::Ins => record.begin - 1 - args.slack_ins, diff --git a/src/strucvars/ingest/mod.rs b/src/strucvars/ingest/mod.rs index 535e9180..925a7168 100644 --- a/src/strucvars/ingest/mod.rs +++ b/src/strucvars/ingest/mod.rs @@ -313,7 +313,7 @@ fn process_variants( // Create temporary directory. We will create one temporary file (containing `jsonl` // seriealized `VarFishStrucvarTsvRecord`s) for each SV type and contig. - let tmp_dir = tempdir::TempDir::new("mehari")?; + let tmp_dir = tempdir::TempDir::new("vfw")?; // Read through input VCF files and write out to temporary files. tracing::info!("converting input VCF files to temporary files..."); diff --git a/src/strucvars/query/interpreter.rs b/src/strucvars/query/interpreter.rs index 0f333d02..26b4200c 100644 --- a/src/strucvars/query/interpreter.rs +++ b/src/strucvars/query/interpreter.rs @@ -1,4 +1,4 @@ -//! Apply settings from a `CaseQuery` to `StructuralVariant` records. +//! Apply settings from a `strucvar::query::schema::CaseQuery` to `StructuralVariant` records. use std::collections::{HashMap, HashSet}; @@ -369,10 +369,6 @@ impl QueryInterpreter { Ok(passes_result) } } - - // TODO: regulatory ensembl/vista - // TODO: regulatory custom - // TODO: recessive mdoe } #[cfg(test)] diff --git a/src/strucvars/query/mod.rs b/src/strucvars/query/mod.rs index c36997fe..053f62e9 100644 --- a/src/strucvars/query/mod.rs +++ b/src/strucvars/query/mod.rs @@ -16,7 +16,6 @@ use std::{ }; use clap::{command, Parser}; -use csv::QuoteStyle; use hgvs::static_data::ASSEMBLY_INFOS; use indexmap::IndexMap; use log::warn; @@ -162,7 +161,6 @@ struct ResultRecord { release: String, chromosome: String, chromosome_no: i32, - // TODO: remove bin bin: u32, chromosome2: String, chromosome_no2: i32, @@ -212,11 +210,12 @@ struct QueryStats { pub by_sv_type: BTreeMap, } -/// Open the SV file at `path_sv_tsv` and run through the given `interpreter`. +/// Run the `args.path_input` VCF file and run through the given `interpreter` writing to +/// `args.path_output`. fn run_query( interpreter: &QueryInterpreter, args: &Args, - dbs: &Databases, + dbs: &InMemoryDbs, mehari_tx_db: &TxSeqDatabase, mehari_tx_idx: &TxIntervalTrees, chrom_to_acc: &HashMap, @@ -226,24 +225,25 @@ fn run_query( let chrom_map = build_chrom_map(); let mut stats = QueryStats::default(); + // Open VCF file, create reader, and read header. let mut input_reader = open_read_maybe_gz(&args.path_input).map_err(|e| { anyhow::anyhow!("could not open file {} for reading: {}", args.path_input, e) })?; let mut input_reader = vcf::Reader::new(&mut input_reader); let input_header = input_reader.read_header()?; + // Create output TSV writer. let mut csv_writer = csv::WriterBuilder::new() .has_headers(true) .delimiter(b'\t') - .quote_style(QuoteStyle::Never) + .quote_style(csv::QuoteStyle::Never) .from_path(&args.path_output)?; // Read through input records using the query interpreter as a filter for input_record in input_reader.records(&input_header) { stats.count_total += 1; - let record_sv: StructuralVariant = - StructuralVariant::from_vcf(&input_record?, &input_header) - .map_err(|e| anyhow::anyhow!("could not parse VCF record: {}", e))?; + let record_sv = StructuralVariant::from_vcf(&input_record?, &input_header) + .map_err(|e| anyhow::anyhow!("could not parse VCF record: {}", e))?; tracing::debug!("processing record {:?}", record_sv); @@ -429,33 +429,36 @@ fn run_query( // Finally, write out the record. let mut uuid_buf = [0u8; 16]; rng.fill_bytes(&mut uuid_buf); - csv_writer.serialize(&ResultRecord { - sodar_uuid: Uuid::from_bytes(uuid_buf), - release: match args.genome_release { - GenomeRelease::Grch37 => "GRCh37".into(), - GenomeRelease::Grch38 => "GRCh38".into(), - }, - chromosome: record_sv.chrom.clone(), - chromosome_no: *chrom_to_chrom_no - .get(&record_sv.chrom) - .expect("invalid chromosome") as i32, - start: record_sv.pos, - bin, - chromosome2: record_sv - .chrom2 - .as_ref() - .unwrap_or(&record_sv.chrom) - .clone(), - chromosome_no2: *chrom_to_chrom_no - .get(&record_sv.chrom) - .expect("invalid chromosome") as i32, - bin2, - end: record_sv.end, - pe_orientation: record_sv.strand_orientation, - sv_type: record_sv.sv_type, - sv_sub_type: record_sv.sv_sub_type, - payload: serde_json::to_string(&result_payload)?, - })?; + csv_writer + .serialize(&ResultRecord { + sodar_uuid: Uuid::from_bytes(uuid_buf), + release: match args.genome_release { + GenomeRelease::Grch37 => "GRCh37".into(), + GenomeRelease::Grch38 => "GRCh38".into(), + }, + chromosome: record_sv.chrom.clone(), + chromosome_no: *chrom_to_chrom_no + .get(&record_sv.chrom) + .expect("invalid chromosome") as i32, + start: record_sv.pos, + bin, + chromosome2: record_sv + .chrom2 + .as_ref() + .unwrap_or(&record_sv.chrom) + .clone(), + chromosome_no2: *chrom_to_chrom_no + .get(&record_sv.chrom) + .expect("invalid chromosome") as i32, + bin2, + end: record_sv.end, + pe_orientation: record_sv.strand_orientation, + sv_type: record_sv.sv_type, + sv_sub_type: record_sv.sv_sub_type, + payload: serde_json::to_string(&result_payload) + .map_err(|e| anyhow::anyhow!("could not serialize payload: {}", e))?, + }) + .map_err(|e| anyhow::anyhow!("could not write record: {}", e))?; } } @@ -821,9 +824,9 @@ pub fn overlapping_hgnc_ids( .collect::>() } -/// Bundle the used database to reduce argument count. +/// Bundle the used in-memory database to reduce argument count. #[derive(Default, Debug)] -pub struct Databases { +pub struct InMemoryDbs { pub bg_dbs: BgDbBundle, pub patho_dbs: PathoDbBundle, pub tad_sets: TadSetBundle, @@ -833,7 +836,10 @@ pub struct Databases { } /// Translate gene allow list to gene identifier sfrom -fn translate_gene_allowlist(gene_allowlist: &Vec, dbs: &Databases) -> HashSet { +pub fn translate_gene_allowlist( + gene_allowlist: &Vec, + dbs: &InMemoryDbs, +) -> HashSet { let mut result = HashSet::new(); let re_entrez = regex::Regex::new(r"^\d+").expect("invalid regex in source code"); @@ -896,12 +902,12 @@ fn translate_gene_allowlist(gene_allowlist: &Vec, dbs: &Databases) -> Ha } /// Load database from the given path with the given genome release. -fn load_databases( +pub fn load_databases( path_worker_db: &str, genome_release: GenomeRelease, max_tad_distance: i32, -) -> Result { - Ok(Databases { +) -> Result { + Ok(InMemoryDbs { bg_dbs: load_bg_dbs(path_worker_db, genome_release)?, patho_dbs: load_patho_dbs(path_worker_db, genome_release)?, tad_sets: load_tads(path_worker_db, genome_release, max_tad_distance)?, @@ -1020,7 +1026,7 @@ pub fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), anyhow: #[cfg(test)] mod test { - // #[tracing_test::traced_test] + #[tracing_test::traced_test] #[test] fn smoke_test() -> Result<(), anyhow::Error> { let tmpdir = temp_testdir::TempDir::default(); diff --git a/src/strucvars/query/schema.rs b/src/strucvars/query/schema.rs index f29e1a12..a59e7bf6 100644 --- a/src/strucvars/query/schema.rs +++ b/src/strucvars/query/schema.rs @@ -1431,7 +1431,7 @@ impl StructuralVariant { } /// Build call information. - pub fn build_call_info( + fn build_call_info( record: &vcf::Record, header: &vcf::Header, ) -> Result, anyhow::Error> { diff --git a/src/strucvars/txt_to_bin/clinvar/input.rs b/src/strucvars/txt_to_bin/clinvar/input.rs index 6e714cae..0ed3c9d2 100644 --- a/src/strucvars/txt_to_bin/clinvar/input.rs +++ b/src/strucvars/txt_to_bin/clinvar/input.rs @@ -257,7 +257,6 @@ impl TryInto for MeasureType { MeasureType::Deletion => Ok(VariationType::Del), MeasureType::Duplication => Ok(VariationType::Dup), MeasureType::TandemDuplication => Ok(VariationType::Dup), - MeasureType::StructuralVariant => todo!(), MeasureType::CopyNumberGain => Ok(VariationType::Dup), MeasureType::CopyNumberLoss => Ok(VariationType::Del), MeasureType::Microsatellite => Ok(VariationType::Microsatellite), @@ -272,6 +271,7 @@ impl TryInto for MeasureType { | MeasureType::ProteinOnly | MeasureType::Fusion | MeasureType::Qtl + | MeasureType::StructuralVariant | MeasureType::Other => anyhow::bail!("unsupported measure type: {:?}", self), } } diff --git a/tests/seqvars/ingest/db/bootstrap.sh b/tests/seqvars/ingest/db/bootstrap.sh index 4b8583cf..67f0017f 100644 --- a/tests/seqvars/ingest/db/bootstrap.sh +++ b/tests/seqvars/ingest/db/bootstrap.sh @@ -31,15 +31,15 @@ mehari \ # clinvar -wget -O /tmp/annonars-clinvar-minimal-grch37-20230910+0.18.0.tar.gz \ - https://github.com/bihealth/annonars-data-clinvar/releases/download/clinvar-weekly-20230910/annonars-clinvar-minimal-grch37-20230910+0.18.0.tar.gz -tar --strip-components 2 -C /tmp -xvf /tmp/annonars-clinvar-minimal-grch37-20230910+0.18.0.tar.gz +wget -O /tmp/annonars-clinvar-minimal-grch37-20231015+0.24.1.tar.gz \ + https://github.com/bihealth/annonars-data-clinvar/releases/download/annonars-data-clinvar-20231015/annonars-clinvar-minimal-grch37-20231015+0.24.1.tar.gz +tar -C /tmp -xvf /tmp/annonars-clinvar-minimal-grch37-20231015+0.24.1.tar.gz mkdir -p $SCRIPT_DIR/grch37/seqvars/clinvar -cp /tmp/annonars-clinvar-minimal-grch37-20230910+0.18.0/spec.yaml \ +cp /tmp/annonars-clinvar-minimal-grch37-20231015+0.24.1/spec.yaml \ $SCRIPT_DIR/grch37/seqvars/clinvar annonars db-utils copy \ - --path-in /tmp/annonars-clinvar-minimal-grch37-20230910+0.18.0/rocksdb \ + --path-in /tmp/annonars-clinvar-minimal-grch37-20231015+0.24.1/rocksdb \ --path-out $SCRIPT_DIR/grch37/seqvars/clinvar/rocksdb \ --range 17:41183866:41337086 diff --git a/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/000014.sst b/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/000014.sst deleted file mode 100644 index 77518c5d..00000000 --- a/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/000014.sst +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:c7f8fc20cf124045d5fdf0050e4af94358f2b25d1b310b205370d5d4dbcc7a50 -size 1343 diff --git a/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/000016.sst b/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/000016.sst deleted file mode 100644 index 89048f37..00000000 --- a/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/000016.sst +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:9735dbd544395502b1ec1a082c7cbfb4abac8e74f23190fc9340ad007d5f1835 -size 248747 diff --git a/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/000036.sst b/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/000036.sst new file mode 100644 index 00000000..542b4e77 --- /dev/null +++ b/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/000036.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:4a7c8e64dc44c6ffbe72cc14d891573f604b08e3fa102c93d0b052cddc44b8ea +size 1343 diff --git a/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/000038.sst b/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/000038.sst new file mode 100644 index 00000000..539c48f4 --- /dev/null +++ b/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/000038.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ef3e4d827895de69c780c98925d010556f3b9885822f9d140d1cec4aad8919e2 +size 588660 diff --git a/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/CURRENT b/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/CURRENT index f8d50486..1a87b731 100644 --- a/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/CURRENT +++ b/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/CURRENT @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:9c283f6e81028b9eb0760d918ee4bc0aa256ed3b926393c1734c760c4bd724fd +oid sha256:501c24889835a42fd2d2fb53dd035809a93ef24302f84936db3099434eb9d5ae size 16 diff --git a/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/LOG b/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/LOG index 790285a0..60553c2e 100644 --- a/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/LOG +++ b/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/LOG @@ -1,3 +1,3 @@ version https://git-lfs.github.com/spec/v1 -oid sha256:b014f43b3d31832f59b85bc8d62c96184f8ee38179e3250c67f34d03e907411b -size 66217 +oid sha256:ecae56e6190c0703cdf8e03724d2e6d1c5d09f250481dbccacdded3a90190bdc +size 64641 diff --git a/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/LOG.old.1697703073190288 b/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/LOG.old.1697703073190288 new file mode 100644 index 00000000..790285a0 --- /dev/null +++ b/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/LOG.old.1697703073190288 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:b014f43b3d31832f59b85bc8d62c96184f8ee38179e3250c67f34d03e907411b +size 66217 diff --git a/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/LOG.old.1697703223234989 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+##SAMPLE= +##SAMPLE= +##SAMPLE= +##PEDIGREE= +##PEDIGREE= +##PEDIGREE= +##x-varfish-case-uuid=00000000-0000-0000-0000-000000000000 +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Case_1_father-N1-DNA1-WGS1 Case_1_index-N1-DNA1-WGS1 Case_1_mother-N1-DNA1-WGS1 +17 41249263 . G A . . gnomad_exomes_an=31398;gnomad_exomes_hom=0;gnomad_exomes_het=56;gnomad_genomes_an=251304;gnomad_genomes_hom=0;gnomad_genomes_het=369;clinvar_clinsig=benign;clinvar_rcv=RCV001353617;ANN=A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/23|c.591C>T|p.C197=|704/7088|591/5592|197/1864|44|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/22|c.450C>T|p.C150=|644/7028|450/5451|150/1817|44|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/22|c.591C>T|p.C197=|698/3696|591/2100|197/700|44|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/24|c.591C>T|p.C197=|704/7151|591/5655|197/1885|44| GT:AD:DP:GQ 0/0:52,0:52:99 0/0:46,0:46:99 0/1:21,21:42:99 +17 41252332 . T C . . ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-435A>G|p.?|555/7088|442/5592||-434|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-435A>G|p.?|495/7028|301/5451||-434|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-435A>G|p.?|549/3696|442/2100||-434|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-435A>G|p.?|555/7151|442/5655||-434| GT:AD:DP:GQ 0/0:25,0:25:75 0/1:14,14:28:99 0/1:19,21:40:99 +17 41252691 . ATATAAT A . . gnomad_exomes_an=2368;gnomad_exomes_hom=10;gnomad_exomes_het=80;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-800_442-795delATTATA|p.?|555/7088|442/5592||-794|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-795delATTATA|p.?|495/7028|301/5451||-794|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-795delATTATA|p.?|549/3696|442/2100||-794|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-795delATTATA|p.?|555/7151|442/5655||-794| GT:AD:DP:GQ 0/0:9,0:9:27 0/1:4,10:14:99 0/1:12,11:23:99 +17 41252693 . ATAAT A . . gnomad_exomes_an=3866;gnomad_exomes_hom=244;gnomad_exomes_het=618;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-800_442-797delATTA|p.?|555/7088|442/5592||-796|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-797delATTA|p.?|495/7028|301/5451||-796|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-797delATTA|p.?|549/3696|442/2100||-796|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-797delATTA|p.?|555/7151|442/5655||-796| GT:AD:DP:GQ 0/0:9,0:9:27 0/0:14,0:14:42 0/1:11,11:22:99 +17 41252695 . AAT A . . gnomad_exomes_an=5066;gnomad_exomes_hom=546;gnomad_exomes_het=795;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-800_442-799delAT|p.?|555/7088|442/5592||-798|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-799delAT|p.?|495/7028|301/5451||-798|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-799delAT|p.?|549/3696|442/2100||-798|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-799delAT|p.?|555/7151|442/5655||-798| GT:AD:DP:GQ 0/1:3,6:9:79 0/0:14,0:14:42 0/0:22,0:22:66 +17 41252696 . A T . . gnomad_exomes_an=4200;gnomad_exomes_hom=29;gnomad_exomes_het=334;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-799T>A|p.?|555/7088|442/5592||-798|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-799T>A|p.?|495/7028|301/5451||-798|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-799T>A|p.?|549/3696|442/2100||-798|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-799T>A|p.?|555/7151|442/5655||-798| GT:AD:DP:GQ 0/1:6,3:9:78 0/1:10,4:14:98 0/0:22,0:22:67 +17 41252697 . A AT . . ANN=AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-801_442-800insA|p.?|555/7088|442/5592||-800|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insA|p.?|495/7028|301/5451||-800|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insA|p.?|549/3696|442/2100||-800|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insA|p.?|555/7151|442/5655||-800| GT:AD:DP:GQ 1/1:0,45:45:99 1/0:16,17:33:99 1/0:22,11:33:99 +17 41252697 . A ATT . . ANN=ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-801_442-800insAA|p.?|555/7088|442/5592||-800|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insAA|p.?|495/7028|301/5451||-800|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insAA|p.?|549/3696|442/2100||-800|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insAA|p.?|555/7151|442/5655||-800| GT:AD:DP:GQ 0/0:45,0:45:99 0/1:17,16:33:99 0/1:12,21:33:99 +17 41254393 . G T . . gnomad_exomes_an=1936;gnomad_exomes_hom=0;gnomad_exomes_het=167;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1746C>A|p.?|554/7088|441/5592||1745|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1746C>A|p.?|494/7028|300/5451||1745|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1746C>A|p.?|548/3696|441/2100||1745|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1746C>A|p.?|554/7151|441/5655||1745| GT:AD:DP:GQ 0/1:29,8:37:66 ./.:.:.:. 0/0:32,3:35:47 +17 41273700 . C CA . . ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2333_80+2334insT|p.?|193/7088|80/5592||2333|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2333_-8+2334insT|p.?|187/7028|-8/5451||2333|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2333_80+2334insT|p.?|187/3696|80/2100||2333|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2333_80+2334insT|p.?|193/7151|80/5655||2333| GT:AD:DP:GQ 0/0:14,0:14:42 0/0:6,1:7:10 0/1:5,5:10:65 +MT 73 . A G . . . GT:AD:DP:GQ 0/0:3975,0:3975:99 1/1:0,2871:2871:99 1/1:0,3320:3320:99 +MT 119 . T C . . . GT:AD:DP:GQ 0/0:5417,1:5418:99 1/1:0,4039:4039:99 1/1:1,4112:4113:99 +MT 189 . A G . . . GT:AD:DP:GQ 0/0:3069,0:3069:99 1/1:0,1721:1721:99 1/1:0,2204:2204:99 +MT 195 . T C . . . GT:AD:DP:GQ 0/0:2599,0:2599:99 1/1:0,1592:1592:99 1/1:0,1815:1815:99 +MT 204 . T C . . . GT:AD:DP:GQ 0/0:2180,0:2180:99 1/1:0,1424:1424:99 1/1:0,1304:1304:99 +MT 207 . G A . . . GT:AD:DP:GQ 0/0:2115,0:2115:99 1/1:0,1408:1408:99 1/1:0,1277:1277:99 +MT 263 . A G . . . GT:AD:DP:GQ 1/1:0,1288:1288:99 1/1:0,1204:1204:99 1/1:0,1031:1031:99 +MT 302 . A ACC . . . GT:AD:DP:GQ 0/1:157,687:844:99 0/0:1005,6:1011:99 0/0:800,3:803:99 +MT 310 . T TC . . . GT:AD:DP:GQ 1/1:0,1035:1035:99 1/1:0,1411:1411:99 1/1:1,1090:1091:99 +MT 477 . T C . . . GT:AD:DP:GQ 1/1:4,2129:2133:99 0/0:2266,1:2267:99 0/0:1725,0:1725:99 +MT 709 . G A . . . GT:AD:DP:GQ 0/0:2494,0:2494:99 1/1:0,2186:2186:99 1/1:1,1813:1814:99 +MT 750 . A G . . . GT:AD:DP:GQ 1/1:0,2757:2757:99 1/1:0,2392:2392:99 1/1:0,1621:1621:99 +MT 879 . T C . . . GT:AD:DP:GQ 0/0:2853,0:2853:99 0/0:2784,0:2784:99 0/1:1351,547:1898:99 +MT 1243 . T C . . . GT:AD:DP:GQ 0/0:2674,1:2675:99 1/1:0,2198:2198:99 1/1:0,1655:1655:99 +MT 1438 . A G . . . GT:AD:DP:GQ 1/1:0,3815:3815:99 1/1:0,3653:3653:99 1/1:0,2900:2900:99 +MT 1824 . T C . . . GT:AD:DP:GQ 1/1:0,2668:2668:99 0/0:2409,0:2409:99 0/0:1752,0:1752:99 +MT 2633 . A G . . . GT:AD:DP:GQ 0/0:2535,0:2535:99 0/1:1648,761:2409:99 0/0:2269,0:2269:99 +MT 2706 . A G . . . GT:AD:DP:GQ 0/0:3200,0:3200:99 1/1:0,2847:2847:99 1/1:0,2020:2020:99 +MT 3010 . G A . . . GT:AD:DP:GQ 1/1:0,2841:2841:99 0/0:2385,0:2385:99 0/0:1685,0:1685:99 +MT 3505 . A G . . . GT:AD:DP:GQ 0/0:2580,14:2594:99 1/1:0,2363:2363:99 1/1:0,1664:1664:99 +MT 3784 . T C . . . GT:AD:DP:GQ 0/1:480,2456:2936:99 0/0:2504,0:2504:99 0/0:1991,0:1991:99 +MT 4769 . A G . . . GT:AD:DP:GQ 1/1:0,2689:2689:99 1/1:0,2549:2549:99 1/1:0,2108:2108:99 +MT 5046 . G A . . . GT:AD:DP:GQ 0/0:2876,2:2878:99 1/1:0,2466:2466:99 1/1:0,1661:1661:99 +MT 5460 . G A . . . GT:AD:DP:GQ 0/0:2905,2:2907:99 1/1:0,2759:2759:99 1/1:2,1968:1970:99 +MT 7028 . C T . . . GT:AD:DP:GQ 0/0:2577,3:2580:99 1/1:2,2201:2203:99 1/1:1,1945:1946:99 +MT 7864 . C T . . . GT:AD:DP:GQ 0/0:3588,1:3589:99 1/1:0,3465:3465:99 1/1:0,2746:2746:99 +MT 8170 . A G . . . GT:AD:DP:GQ 0/0:2051,1:2052:99 1/1:0,2257:2257:99 1/1:0,1774:1774:99 +MT 8251 . G A . . . GT:AD:DP:GQ 0/0:2360,0:2360:99 1/1:0,2317:2317:99 1/1:1,1624:1625:99 +MT 8860 . A G . . . GT:AD:DP:GQ 1/1:0,3278:3278:99 1/1:0,3088:3088:99 1/1:0,2241:2241:99 +MT 8994 . G A . . . GT:AD:DP:GQ 0/0:2793,0:2793:99 1/1:0,2368:2368:99 1/1:1,1917:1918:99 +MT 9007 . A G . . . GT:AD:DP:GQ 1/1:0,2959:2959:99 0/0:2442,0:2442:99 0/0:1735,0:1735:99 +MT 9150 . A G . . . GT:AD:DP:GQ 1/1:0,3163:3163:99 0/0:3538,0:3538:99 0/0:2767,0:2767:99 +MT 9380 . G A . . . GT:AD:DP:GQ 1/1:1,3320:3321:99 0/0:3222,0:3222:99 0/0:2547,0:2547:99 +MT 10097 . A G . . . GT:AD:DP:GQ 0/0:2660,0:2660:99 0/1:1680,508:2188:99 0/0:1851,0:1851:99 +MT 11204 . T C . . . GT:AD:DP:GQ 0/0:3168,5:3173:99 1/1:0,2922:2922:99 1/1:0,2418:2418:99 +MT 11674 . C T . . . GT:AD:DP:GQ 0/0:2890,0:2890:99 1/1:0,2666:2666:99 1/1:1,2179:2180:99 +MT 11719 . G A . . . GT:AD:DP:GQ 0/0:3339,2:3341:99 1/1:0,3052:3052:99 1/1:0,2203:2203:99 +MT 11947 . A G . . . GT:AD:DP:GQ 0/0:2579,2:2581:99 1/1:0,2273:2273:99 1/1:0,1804:1804:99 +MT 12414 . T C . . . GT:AD:DP:GQ 0/0:2852,3:2855:99 1/1:1,2545:2546:99 1/1:0,1733:1733:99 +MT 12648 . A G . . . GT:AD:DP:GQ 0/0:1812,1:1813:99 1/1:2,1662:1664:99 1/1:4,1777:1781:99 +MT 12705 . C T . . . GT:AD:DP:GQ 0/0:2359,10:2369:99 1/1:1,2137:2138:99 1/1:1,1621:1622:99 +MT 13406 . G A . . . GT:AD:DP:GQ 0/0:2539,1:2540:99 0/0:2216,0:2216:99 0/1:1224,733:1957:99 +MT 13611 . A G . . . GT:AD:DP:GQ 0/0:3838,2:3840:99 1/1:0,3717:3717:99 1/1:1,2834:2835:99 +MT 13928 . G C . . . GT:AD:DP:GQ 0/0:2947,0:2947:99 1/1:0,2700:2700:99 1/1:0,1880:1880:99 +MT 14148 . A G . . . GT:AD:DP:GQ 0/0:3019,2:3021:99 1/1:0,2820:2820:99 1/1:0,1962:1962:99 +MT 14766 . C T . . . GT:AD:DP:GQ 0/0:3318,3:3321:99 1/1:2,3111:3113:99 1/1:3,2355:2358:99 +MT 15326 . A G . . . GT:AD:DP:GQ 1/1:0,3716:3716:99 1/1:0,3560:3560:99 1/1:0,2690:2690:99 +MT 15884 . G C . . . GT:AD:DP:GQ 0/0:3595,1:3596:99 1/1:0,3167:3167:99 1/1:1,2733:2734:99 +MT 16184 . C T . . . GT:AD:DP:GQ 0/0:1406,1:1407:99 1/1:0,1969:1969:99 1/1:0,1478:1478:99 +MT 16223 . C T . . . GT:AD:DP:GQ 0/0:1405,1:1406:99 1/1:0,2018:2018:99 1/1:0,1472:1472:99 +MT 16263 . T C . . . GT:AD:DP:GQ 1/1:2,1476:1478:99 0/0:1994,0:1994:99 0/0:1475,0:1475:99 +MT 16292 . C T . . . GT:AD:DP:GQ 0/0:1652,0:1652:99 1/1:1,1913:1914:99 1/1:0,1476:1476:99 +MT 16519 . T C . . . GT:AD:DP:GQ 1/1:0,1759:1759:99 1/1:0,4094:4094:99 1/1:0,1744:1744:99 diff --git a/tests/seqvars/query/Case_1.query.json b/tests/seqvars/query/Case_1.query.json new file mode 100644 index 00000000..02d583db --- /dev/null +++ b/tests/seqvars/query/Case_1.query.json @@ -0,0 +1,121 @@ +{ + "effects": [ + "chromosome_number_variation", + "exon_loss_variant", + "frameshift_variant", + "rare_amino_acid_variant", + "splice_acceptor_variant", + "splice_donor_variant", + "start_lost", + "stop_gained", + "stop_lost", + "transcript_ablation", + "3_prime_UTR_truncation", + "5_prime_UTR_truncation", + "conservative_inframe_deletion", + "conservative_inframe_insertion", + "disruptive_inframe_deletion", + "disruptive_inframe_insertion", + "missense_variant", + "regulatory_region_ablation", + "splice_region_variant", + "TFBS_ablation", + "5_prime_UTR_premature_start_codon_gain_variant", + "initiator_codon_variant", + "start_retained", + "stop_retained_variant", + "synonymous_variant", + "3_prime_UTR_variant", + "5_prime_UTR_variant", + "coding_sequence_variant", + "conserved_intergenic_variant", + "conserved_intron_variant", + "downstream_gene_variant", + "exon_variant", + "feature_elongation", + "feature_truncation", + "gene_variant", + "intergenic_variant", + "intron_variant", + "mature_miRNA_variant", + "miRNA", + "NMD_transcript_variant", + "non_coding_transcript_exon_variant", + "non_coding_transcript_intron_variant", + "regulatory_region_amplification", + "regulatory_region_variant", + "TF_binding_site_variant", + "TFBS_amplification", + "transcript_amplification", + "transcript_variant", + "upstream_gene_variant" + ], + "gnomad_exomes_enabled": false, + "gnomad_genomes_enabled": false, + "inhouse_enabled": false, + "helixmtdb_enabled": false, + "quality": { + "Case_1_index-N1-DNA1-WGS1": { + "dp_het": 10, + "dp_hom": 5, + "gq": 10, + "ab": 0.2, + "ad": 3, + "ad_max": null, + "fail": "drop-variant" + }, + "Case_1_father-N1-DNA1-WGS1": { + "dp_het": 10, + "dp_hom": 5, + "gq": 10, + "ab": 0.2, + "ad": 3, + "ad_max": null, + "fail": "drop-variant" + }, + "Case_1_mother-N1-DNA1-WGS1": { + "dp_het": 10, + "dp_hom": 5, + "gq": 10, + "ab": 0.2, + "ad": 3, + "ad_max": null, + "fail": "drop-variant" + } + }, + "genotype": { + "Case_1_index-N1-DNA1-WGS1": "any", + "Case_1_father-N1-DNA1-WGS1": "any", + "Case_1_mother-N1-DNA1-WGS1": "any" + }, + "selected_variants": null, + "transcripts_coding": true, + "transcripts_noncoding": true, + "var_type_snv": true, + "var_type_indel": true, + "var_type_mnv": true, + "max_exon_dist": 100, + "gene_allowlist": [], + "genomic_regions": null, + "require_in_clinvar": false, + "clinvar_include_benign": false, + "clinvar_include_pathogenic": true, + "clinvar_include_likely_benign": false, + "clinvar_include_likely_pathogenic": true, + "clinvar_include_uncertain_significance": false, + "gnomad_exomes_frequency": 0.002, + "gnomad_exomes_heterozygous": 20, + "gnomad_exomes_homozygous": 0, + "gnomad_exomes_hemizygous": null, + "gnomad_genomes_frequency": 0.002, + "gnomad_genomes_heterozygous": 4, + "gnomad_genomes_homozygous": 0, + "gnomad_genomes_hemizygous": null, + "inhouse_carriers": 20, + "inhouse_heterozygous": null, + "inhouse_homozygous": null, + "inhouse_hemizygous": null, + "helixmtdb_frequency": 0.01, + "helixmtdb_heterozygous": null, + "helixmtdb_homozygous": null +} diff --git a/tests/seqvars/query/Case_1.query.json.bak b/tests/seqvars/query/Case_1.query.json.bak new file mode 100644 index 00000000..61299783 --- /dev/null +++ b/tests/seqvars/query/Case_1.query.json.bak @@ -0,0 +1,121 @@ +{ + "effects": [ + "chromosome_number_variation", + "exon_loss_variant", + "frameshift_variant", + "rare_amino_acid_variant", + "splice_acceptor_variant", + "splice_donor_variant", + "start_lost", + "stop_gained", + "stop_lost", + "transcript_ablation", + "3_prime_UTR_truncation", + "5_prime_UTR_truncation", + "conservative_inframe_deletion", + "conservative_inframe_insertion", + "disruptive_inframe_deletion", + "disruptive_inframe_insertion", + "missense_variant", + "regulatory_region_ablation", + "splice_region_variant", + "TFBS_ablation", + "5_prime_UTR_premature_start_codon_gain_variant", + "initiator_codon_variant", + "start_retained", + "stop_retained_variant", + "synonymous_variant", + "3_prime_UTR_variant", + "5_prime_UTR_variant", + "coding_sequence_variant", + "conserved_intergenic_variant", + "conserved_intron_variant", + "downstream_gene_variant", + "exon_variant", + "feature_elongation", + "feature_truncation", + "gene_variant", + "intergenic_variant", + "intron_variant", + "mature_miRNA_variant", + "miRNA", + "NMD_transcript_variant", + "non_coding_transcript_exon_variant", + "non_coding_transcript_intron_variant", + "regulatory_region_amplification", + "regulatory_region_variant", + "TF_binding_site_variant", + "TFBS_amplification", + "transcript_amplification", + "transcript_variant", + "upstream_gene_variant" + ], + "gnomad_exomes_enabled": false, + "gnomad_genomes_enabled": false, + "inhouse_enabled": false, + "helixmtdb_enabled": false, + "quality": { + "Case_1_index-N1-DNA1-WGS1": { + "dp_het": 10, + "dp_hom": 5, + "gq": 10, + "ab": 0.2, + "ad": 3, + "ad_max": null, + "fail": "drop-variant" + }, + "Case_1_father-N1-DNA1-WGS1": { + "dp_het": 10, + "dp_hom": 5, + "gq": 10, + "ab": 0.2, + "ad": 3, + "ad_max": null, + "fail": "drop-variant" + }, + "Case_1_mother-N1-DNA1-WGS1": { + "dp_het": 10, + "dp_hom": 5, + "gq": 10, + "ab": 0.2, + "ad": 3, + "ad_max": null, + "fail": "drop-variant" + } + }, + "genotype": { + "Case_1_index-N1-DNA1-WGS1": "variant", + "Case_1_father-N1-DNA1-WGS1": "ref", + "Case_1_mother-N1-DNA1-WGS1": "ref" + }, + "selected_variants": null, + "transcripts_coding": true, + "transcripts_noncoding": true, + "var_type_snv": true, + "var_type_indel": true, + "var_type_mnv": true, + "max_exon_dist": 100, + "gene_allowlist": [], + "genomic_regions": null, + "require_in_clinvar": false, + "clinvar_include_benign": false, + "clinvar_include_pathogenic": true, + "clinvar_include_likely_benign": false, + "clinvar_include_likely_pathogenic": true, + "clinvar_include_uncertain_significance": false, + "gnomad_exomes_frequency": 0.002, + "gnomad_exomes_heterozygous": 20, + "gnomad_exomes_homozygous": 0, + "gnomad_exomes_hemizygous": null, + "gnomad_genomes_frequency": 0.002, + "gnomad_genomes_heterozygous": 4, + "gnomad_genomes_homozygous": 0, + "gnomad_genomes_hemizygous": null, + "inhouse_carriers": 20, + "inhouse_heterozygous": null, + "inhouse_homozygous": null, + "inhouse_hemizygous": null, + "helixmtdb_frequency": 0.01, + "helixmtdb_heterozygous": null, + "helixmtdb_homozygous": null +} diff --git a/tests/seqvars/query/db b/tests/seqvars/query/db new file mode 120000 index 00000000..eafeccfd --- /dev/null +++ b/tests/seqvars/query/db @@ -0,0 +1 @@ +../../strucvars/query/db \ No newline at end of file diff --git a/tests/seqvars/query/dragen.ingested.vcf b/tests/seqvars/query/dragen.ingested.vcf new file mode 100644 index 00000000..757d38a3 --- /dev/null +++ b/tests/seqvars/query/dragen.ingested.vcf @@ -0,0 +1,53 @@ +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##fileDate=20230421 +##SAMPLE= +##PEDIGREE= +##x-varfish-case-uuid=00000000-0000-0000-0000-000000000000 +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CASE +17 41256074 . CA C . . gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+64delT|p.?|554/7088|441/5592||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||63| GT:AD:DP:GQ:PS 1|1:0,80:80:99:41256074 +MT 750 . A G . . . GT:AD:DP:GQ 1/1:0,35:35:99 diff --git a/tests/seqvars/query/dragen.query.json b/tests/seqvars/query/dragen.query.json new file mode 100644 index 00000000..568e5e3d --- /dev/null +++ b/tests/seqvars/query/dragen.query.json @@ -0,0 +1,101 @@ +{ + "effects": [ + "chromosome_number_variation", + "exon_loss_variant", + "frameshift_variant", + "rare_amino_acid_variant", + "splice_acceptor_variant", + "splice_donor_variant", + "start_lost", + "stop_gained", + "stop_lost", + "transcript_ablation", + "3_prime_UTR_truncation", + "5_prime_UTR_truncation", + "conservative_inframe_deletion", + "conservative_inframe_insertion", + "disruptive_inframe_deletion", + "disruptive_inframe_insertion", + "missense_variant", + "regulatory_region_ablation", + "splice_region_variant", + "TFBS_ablation", + "5_prime_UTR_premature_start_codon_gain_variant", + "initiator_codon_variant", + "start_retained", + "stop_retained_variant", + "synonymous_variant", + "3_prime_UTR_variant", + "5_prime_UTR_variant", + "coding_sequence_variant", + "conserved_intergenic_variant", + "conserved_intron_variant", + "downstream_gene_variant", + "exon_variant", + "feature_elongation", + "feature_truncation", + "gene_variant", + "intergenic_variant", + "intron_variant", + "mature_miRNA_variant", + "miRNA", + "NMD_transcript_variant", + "non_coding_transcript_exon_variant", + "non_coding_transcript_intron_variant", + "regulatory_region_amplification", + "regulatory_region_variant", + "TF_binding_site_variant", + "TFBS_amplification", + "transcript_amplification", + "transcript_variant", + "upstream_gene_variant" + ], + "gnomad_exomes_enabled": false, + "gnomad_genomes_enabled": false, + "inhouse_enabled": false, + "helixmtdb_enabled": false, + "quality": { + "CASE": { + "dp_het": 10, + "dp_hom": 5, + "gq": 10, + "ab": 0.2, + "ad": 3, + "ad_max": null, + "fail": "drop-variant" + } + }, + "genotype": { + "CASE": "variant" + }, + "selected_variants": null, + "transcripts_coding": true, + "transcripts_noncoding": true, + "var_type_snv": true, + "var_type_indel": true, + "var_type_mnv": true, + "max_exon_dist": 100, + "gene_allowlist": [], + "genomic_regions": null, + "require_in_clinvar": false, + "clinvar_include_benign": false, + "clinvar_include_pathogenic": true, + "clinvar_include_likely_benign": false, + "clinvar_include_likely_pathogenic": true, + "clinvar_include_uncertain_significance": false, + "gnomad_exomes_frequency": 0.002, + "gnomad_exomes_heterozygous": 20, + "gnomad_exomes_homozygous": 0, + "gnomad_exomes_hemizygous": null, + "gnomad_genomes_frequency": 0.002, + "gnomad_genomes_heterozygous": 4, + "gnomad_genomes_homozygous": 0, + "gnomad_genomes_hemizygous": null, + "inhouse_carriers": 20, + "inhouse_heterozygous": null, + "inhouse_homozygous": null, + "inhouse_hemizygous": null, + "helixmtdb_frequency": 0.01, + "helixmtdb_heterozygous": null, + "helixmtdb_homozygous": null +} diff --git a/tests/seqvars/query/empty.json b/tests/seqvars/query/empty.json new file mode 100644 index 00000000..0967ef42 --- /dev/null +++ b/tests/seqvars/query/empty.json @@ -0,0 +1 @@ +{} diff --git a/tests/seqvars/query/full.json b/tests/seqvars/query/full.json new file mode 100644 index 00000000..743cd7d9 --- /dev/null +++ b/tests/seqvars/query/full.json @@ -0,0 +1,85 @@ +{ + "effects": [ + "3_prime_UTR_exon_variant", + "3_prime_UTR_intron_variant", + "5_prime_UTR_exon_variant", + "5_prime_UTR_intron_variant", + "coding_transcript_intron_variant", + "complex_substitution", + "direct_tandem_duplication", + "disruptive_inframe_deletion", + "disruptive_inframe_insertion", + "downstream_gene_variant", + "exon_loss_variant", + "feature_truncation", + "frameshift_elongation", + "frameshift_truncation", + "frameshift_variant", + "inframe_deletion", + "inframe_insertion", + "internal_feature_elongation", + "missense_variant", + "mnv", + "non_coding_transcript_exon_variant", + "non_coding_transcript_intron_variant", + "splice_acceptor_variant", + "splice_donor_variant", + "splice_region_variant", + "start_lost", + "stop_gained", + "stop_lost", + "stop_retained_variant", + "structural_variant", + "synonymous_variant", + "transcript_ablation", + "upstream_gene_variant" + ], + "gnomad_exomes_enabled": true, + "gnomad_genomes_enabled": true, + "inhouse_enabled": true, + "helixmtdb_enabled": true, + "quality": { + "sample": { + "dp_het": 10, + "dp_hom": 5, + "gq": 10, + "ab": 0.2, + "ad": 3, + "ad_max": null, + "fail": "drop-variant" + } + }, + "genotype": { + "sample": "het" + }, + "selected_variants": null, + "transcripts_coding": true, + "transcripts_noncoding": true, + "var_type_snv": true, + "var_type_indel": true, + "var_type_mnv": true, + "max_exon_dist": 100, + "gene_allowlist": [], + "genomic_regions": null, + "require_in_clinvar": false, + "clinvar_include_benign": false, + "clinvar_include_pathogenic": true, + "clinvar_include_likely_benign": false, + "clinvar_include_likely_pathogenic": true, + "clinvar_include_uncertain_significance": false, + "gnomad_exomes_frequency": 0.002, + "gnomad_exomes_heterozygous": 20, + "gnomad_exomes_homozygous": 0, + "gnomad_exomes_hemizygous": null, + "gnomad_genomes_frequency": 0.002, + "gnomad_genomes_heterozygous": 4, + "gnomad_genomes_homozygous": 0, + "gnomad_genomes_hemizygous": null, + "inhouse_carriers": 20, + "inhouse_heterozygous": null, + "inhouse_homozygous": null, + "inhouse_hemizygous": null, + "helixmtdb_frequency": 0.01, + "helixmtdb_heterozygous": null, + "helixmtdb_homozygous": null +} diff --git a/tests/seqvars/query/with_extra.json b/tests/seqvars/query/with_extra.json new file mode 100644 index 00000000..1a9d62fb --- /dev/null +++ b/tests/seqvars/query/with_extra.json @@ -0,0 +1,86 @@ +{ + "__some_extra__": "42", + "effects": [ + "3_prime_UTR_exon_variant", + "3_prime_UTR_intron_variant", + "5_prime_UTR_exon_variant", + "5_prime_UTR_intron_variant", + "coding_transcript_intron_variant", + "complex_substitution", + "direct_tandem_duplication", + "disruptive_inframe_deletion", + "disruptive_inframe_insertion", + "downstream_gene_variant", + "exon_loss_variant", + "feature_truncation", + "frameshift_elongation", + "frameshift_truncation", + "frameshift_variant", + "inframe_deletion", + "inframe_insertion", + "internal_feature_elongation", + "missense_variant", + "mnv", + "non_coding_transcript_exon_variant", + "non_coding_transcript_intron_variant", + "splice_acceptor_variant", + "splice_donor_variant", + "splice_region_variant", + "start_lost", + "stop_gained", + "stop_lost", + "stop_retained_variant", + "structural_variant", + "synonymous_variant", + "transcript_ablation", + "upstream_gene_variant" + ], + "gnomad_exomes_enabled": true, + "gnomad_genomes_enabled": true, + "inhouse_enabled": true, + "helixmtdb_enabled": true, + "quality": { + "sample": { + "dp_het": 10, + "dp_hom": 5, + "gq": 10, + "ab": 0.2, + "ad": 3, + "ad_max": null, + "fail": "drop-variant" + } + }, + "genotype": { + "sample": "het" + }, + "selected_variants": null, + "transcripts_coding": true, + "transcripts_noncoding": true, + "var_type_snv": true, + "var_type_indel": true, + "var_type_mnv": true, + "max_exon_dist": 100, + "gene_allowlist": [], + "genomic_regions": null, + "require_in_clinvar": false, + "clinvar_include_benign": false, + "clinvar_include_pathogenic": true, + "clinvar_include_likely_benign": false, + "clinvar_include_likely_pathogenic": true, + "clinvar_include_uncertain_significance": false, + "gnomad_exomes_frequency": 0.002, + "gnomad_exomes_heterozygous": 20, + "gnomad_exomes_homozygous": 0, + "gnomad_exomes_hemizygous": null, + "gnomad_genomes_frequency": 0.002, + "gnomad_genomes_heterozygous": 4, + "gnomad_genomes_homozygous": 0, + "gnomad_genomes_hemizygous": null, + "inhouse_carriers": 20, + "inhouse_heterozygous": null, + "inhouse_homozygous": null, + "inhouse_hemizygous": null, + "helixmtdb_frequency": 0.01, + "helixmtdb_heterozygous": null, + "helixmtdb_homozygous": null +} diff --git a/tests/strucvars/query/bootstrap.sh b/tests/strucvars/query/bootstrap.sh index 549236b9..c7f4f8b6 100644 --- a/tests/strucvars/query/bootstrap.sh +++ b/tests/strucvars/query/bootstrap.sh @@ -17,6 +17,7 @@ TXT_TO_BIN="cargo run --release -- strucvars txt-to-bin --assembly=grch37" mkdir -p $SCRIPT_DIR/db/worker/grch37/{features,genes,strucvars/bgdbs,tads} mkdir -p $SCRIPT_DIR/db/worker/noref/genes mkdir -p $SCRIPT_DIR/db/mehari/grch37 +mkdir -p $SCRIPT_DIR/db/annonars/grch37 # Filter BED files filter-bed() @@ -31,6 +32,28 @@ write-to() tee $1 >/dev/null } +# annonars/genes + +cp -r $SRC/annonars/genes-3.1+2.1.1+4.4+20230606+10.1+20230913+0.19.0 tests/seqvars/query/db/annonars/genes + +# annonars/grch37 + +SRC_ANNONARS=$SRC/annonars +for src in $SRC_ANNONARS/*-grch37*; do + if [[ $src == *c+* ]] || [[ $src == *gnomad* ]]; then + continue + fi + cp -r $src $SCRIPT_DIR/db/annonars/grch37/$(basename ${src%-grch37*}) +done + +# annonars/grch37/clinvar-minimal + +pushd /tmp +wget https://github.com/bihealth/annonars-data-clinvar/releases/download/clinvar-weekly-20230910/annonars-clinvar-minimal-grch37-20230910+0.18.0.tar.gz +tar -vxf annonars-clinvar-minimal-grch37-20230910+0.18.0.tar.gz +mv tmp/for-upload/annonars-clinvar-minimal-grch37-20230910+0.18.0 $SCRIPT_DIR/db/annonars/grch37/clinvar-minimal +popd + # mehari/grch37/ mkdir -p /tmp/mehari-data-grch37 diff --git a/tests/strucvars/query/db/annonars/genes/rocksdb/000014.sst b/tests/strucvars/query/db/annonars/genes/rocksdb/000014.sst new file mode 100644 index 00000000..0266aaeb --- /dev/null +++ b/tests/strucvars/query/db/annonars/genes/rocksdb/000014.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:942aed55caf93257a5708d0fc6bac2aec78b397843224edd7ea1b2e0e5b44e28 +size 1284 diff --git a/tests/strucvars/query/db/annonars/genes/rocksdb/000016.sst b/tests/strucvars/query/db/annonars/genes/rocksdb/000016.sst new file mode 100644 index 00000000..1c405661 --- /dev/null +++ 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