From 322c61679a604d6b6cd54865bf6dc255d6d0df86 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Mon, 12 Sep 2022 13:55:35 +0200 Subject: [PATCH] Adding end-to-end tests hg19-chr22 (#61) Closes: #61 Related-Issue: #61 Projected-Results-Impact: none --- .gitattributes | 3 + .github/workflows/ci.yml | 15 +- CHANGES.md | 2 + README.md | 12 ++ tests/hg19-chr22/.gitignore | 6 + ...ncall_integrated_v5b.20130502.sites.vcf.gz | 3 + ...l_integrated_v5b.20130502.sites.vcf.gz.tbi | 3 + .../Case_1_index.delly2.db-info.tsv-expected | 9 + ..._index.delly2.feature-effects.tsv-expected | 1 + .../Case_1_index.delly2.gts.tsv-expected | 1 + tests/hg19-chr22/Case_1_index.delly2.vcf.gz | 3 + .../hg19-chr22/Case_1_index.delly2.vcf.gz.tbi | 3 + .../Case_1_index.gatk_hc.db-info.tsv-expected | 9 + .../Case_1_index.gatk_hc.gts.tsv-expected | 167 ++++++++++++++++++ tests/hg19-chr22/Case_1_index.gatk_hc.vcf.gz | 3 + .../Case_1_index.gatk_hc.vcf.gz.tbi | 3 + tests/hg19-chr22/Clinvar.tsv | 1 + tests/hg19-chr22/Clinvar.tsv.gz | Bin 0 -> 36538 bytes tests/hg19-chr22/ExAC.r1.sites.vep.vcf.gz | 3 + tests/hg19-chr22/ExAC.r1.sites.vep.vcf.gz.tbi | 3 + tests/hg19-chr22/HgmdPublicLocus.tsv.gz | Bin 0 -> 187 bytes tests/hg19-chr22/build.sh | 119 +++++++++++++ tests/hg19-chr22/chr22_part.fa.fai | 3 + tests/hg19-chr22/chr22_part.fa.gz | 3 + tests/hg19-chr22/db-info.txt-expected | 12 ++ .../gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz | 3 + ...omad.exomes.r2.1.1.sites.chr22.vcf.bgz.tbi | 3 + .../gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz | 3 + ...mad.genomes.r2.1.1.sites.chr22.vcf.bgz.tbi | 3 + tests/hg19-chr22/hg19_ensembl.ser | 3 + tests/hg19-chr22/hg19_refseq.ser | 3 + tests/hg19-chr22/run-tests.sh | 94 ++++++++++ .../VarfishAnnotatorCli.java | 3 + .../annotate/AnnotateArgs.java | 12 ++ .../annotate/AnnotateVcf.java | 3 +- .../annotate_svs/AnnotateSvsArgs.java | 12 ++ .../annotate_svs/AnnotateSvsVcf.java | 3 +- .../utils/DatabaseSelfTest.java | 5 +- 38 files changed, 531 insertions(+), 6 deletions(-) create mode 100644 .gitattributes create mode 100644 tests/hg19-chr22/.gitignore create mode 100644 tests/hg19-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz create mode 100644 tests/hg19-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz.tbi create mode 100644 tests/hg19-chr22/Case_1_index.delly2.db-info.tsv-expected create mode 100644 tests/hg19-chr22/Case_1_index.delly2.feature-effects.tsv-expected create mode 100644 tests/hg19-chr22/Case_1_index.delly2.gts.tsv-expected create mode 100644 tests/hg19-chr22/Case_1_index.delly2.vcf.gz create mode 100644 tests/hg19-chr22/Case_1_index.delly2.vcf.gz.tbi create mode 100644 tests/hg19-chr22/Case_1_index.gatk_hc.db-info.tsv-expected create mode 100644 tests/hg19-chr22/Case_1_index.gatk_hc.gts.tsv-expected create mode 100644 tests/hg19-chr22/Case_1_index.gatk_hc.vcf.gz create mode 100644 tests/hg19-chr22/Case_1_index.gatk_hc.vcf.gz.tbi create mode 100644 tests/hg19-chr22/Clinvar.tsv create mode 100644 tests/hg19-chr22/Clinvar.tsv.gz create mode 100644 tests/hg19-chr22/ExAC.r1.sites.vep.vcf.gz create mode 100644 tests/hg19-chr22/ExAC.r1.sites.vep.vcf.gz.tbi create mode 100644 tests/hg19-chr22/HgmdPublicLocus.tsv.gz create mode 100755 tests/hg19-chr22/build.sh create mode 100644 tests/hg19-chr22/chr22_part.fa.fai create mode 100644 tests/hg19-chr22/chr22_part.fa.gz create mode 100644 tests/hg19-chr22/db-info.txt-expected create mode 100644 tests/hg19-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz create mode 100644 tests/hg19-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz.tbi create mode 100644 tests/hg19-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz create mode 100644 tests/hg19-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz.tbi create mode 100644 tests/hg19-chr22/hg19_ensembl.ser create mode 100644 tests/hg19-chr22/hg19_refseq.ser create mode 100755 tests/hg19-chr22/run-tests.sh diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..676beb5 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,3 @@ +/tests/**/*.fa* filter=lfs diff=lfs merge=lfs -text +/tests/**/*.ser filter=lfs diff=lfs merge=lfs -text +/tests/**/*.vcf* filter=lfs diff=lfs merge=lfs -text diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7907e8c..47faa70 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -49,19 +49,28 @@ jobs: steps: - uses: actions/checkout@v2 + with: + lfs: true + - name: Check out LFS objects + run: git lfs fetch --all - name: Set up JDK uses: actions/setup-java@v2 with: java-version: ${{ matrix.java }} distribution: 'adopt' - - name: Build with Maven and submit coverage report + - name: Build JAR with Maven without submitting coverage report run: > mvn --batch-mode --update-snapshots clean - test + package + + - name: Run end-to-end tests + run: | + cd tests/hg19-chr22 + bash run-tests.sh testing-coverage: runs-on: ubuntu-latest @@ -78,7 +87,7 @@ jobs: java-version: ${{ matrix.java }} distribution: 'adopt' - - name: Build with Maven and submit coverage report + - name: Run test with Maven and submit coverage report run: > mvn --define repoToken=${{ secrets.COVERALLS_REPO_TOKEN }} diff --git a/CHANGES.md b/CHANGES.md index ff6ea12..2ec6d37 100644 --- a/CHANGES.md +++ b/CHANGES.md @@ -2,6 +2,8 @@ ## v0.26-SNAPSHOT +- Adding end-to-end tests `hg19-chr22` (#61) + ## v0.25 - Fixing unresolved issue with self-test (#51, #56) diff --git a/README.md b/README.md index b3eb233..9cf1fd3 100644 --- a/README.md +++ b/README.md @@ -62,3 +62,15 @@ The following will create `varfish-annotator-db-1906.h2.db` and fill it. ``` # mvn com.coveo:fmt-maven-plugin:format -Dverbose=true ``` + +## Tests + +The folder `/tests` contains some data sets that are appropriate for system (aka "end-to-end") tests of the software. + +- `hg19-chr22` -- + This folder contains examples for annotating GATK HC and Delly2 calls on the first 20MB of chr22. + Only the variants overlapping with `ADA2` and `GAB4` are used. + +You can build the data sets with the `build.sh` script that is available in each folder. +This script also serves for documenting the test data's provenance. +The Jannovar software must be available as `jannovar` (e.g., through bioconda) on your `PATH` and you will need `samtools`. diff --git a/tests/hg19-chr22/.gitignore b/tests/hg19-chr22/.gitignore new file mode 100644 index 0000000..ceba6c3 --- /dev/null +++ b/tests/hg19-chr22/.gitignore @@ -0,0 +1,6 @@ +*.tmp + +chr22.* +chr22_part.fa + +/data diff --git a/tests/hg19-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz b/tests/hg19-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz new file mode 100644 index 0000000..0e79641 --- /dev/null +++ b/tests/hg19-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2373ace9968bd79b0d04f00d91430cf72ca57b05fe05d8a530bdcd5afeefdfe2 +size 90718 diff --git a/tests/hg19-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz.tbi b/tests/hg19-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz.tbi new file mode 100644 index 0000000..c80e3cd --- /dev/null +++ b/tests/hg19-chr22/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz.tbi @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a41f62107618ddf1f852658bf2d62b32b80f41947360c407c479782e34f65225 +size 238 diff --git a/tests/hg19-chr22/Case_1_index.delly2.db-info.tsv-expected b/tests/hg19-chr22/Case_1_index.delly2.db-info.tsv-expected new file mode 100644 index 0000000..9d765e2 --- /dev/null +++ b/tests/hg19-chr22/Case_1_index.delly2.db-info.tsv-expected @@ -0,0 +1,9 @@ +genomebuild db_name release +GRCh37 clinvar for-testing +GRCh37 exac r1.0 +GRCh37 gnomad_exomes r2.1.1 +GRCh37 gnomad_genomes r2.1.1 +GRCh37 hgmd_public for-testing +GRCh37 thousand_genomes v3.20101123 +GRCh37 varfish-annotator 0.26-SNAPSHOT +GRCh37 varfish-annotator-db for-testing diff --git a/tests/hg19-chr22/Case_1_index.delly2.feature-effects.tsv-expected b/tests/hg19-chr22/Case_1_index.delly2.feature-effects.tsv-expected new file mode 100644 index 0000000..33dfc21 --- /dev/null +++ b/tests/hg19-chr22/Case_1_index.delly2.feature-effects.tsv-expected @@ -0,0 +1 @@ +case_id set_id sv_uuid refseq_gene_id refseq_transcript_id refseq_transcript_coding refseq_effect ensembl_gene_id ensembl_transcript_id ensembl_transcript_coding ensembl_effect diff --git a/tests/hg19-chr22/Case_1_index.delly2.gts.tsv-expected b/tests/hg19-chr22/Case_1_index.delly2.gts.tsv-expected new file mode 100644 index 0000000..bd26df5 --- /dev/null +++ b/tests/hg19-chr22/Case_1_index.delly2.gts.tsv-expected @@ -0,0 +1 @@ +release chromosome chromosome_no bin chromosome2 chromosome_no2 bin2 pe_orientation start end start_ci_left start_ci_right end_ci_left end_ci_right case_id set_id sv_uuid caller sv_type sv_sub_type info num_hom_alt num_hom_ref num_het num_hemi_alt num_hemi_ref genotype diff --git a/tests/hg19-chr22/Case_1_index.delly2.vcf.gz b/tests/hg19-chr22/Case_1_index.delly2.vcf.gz new file mode 100644 index 0000000..823af83 --- /dev/null +++ b/tests/hg19-chr22/Case_1_index.delly2.vcf.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1db4d69d5e29cf927a33b6913bc9a54a7207c8c4c6f37de80daafbb7c7ad6d78 +size 3184 diff --git a/tests/hg19-chr22/Case_1_index.delly2.vcf.gz.tbi b/tests/hg19-chr22/Case_1_index.delly2.vcf.gz.tbi new file mode 100644 index 0000000..d40d305 --- /dev/null +++ b/tests/hg19-chr22/Case_1_index.delly2.vcf.gz.tbi @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:eafcf2285c7c3e55c2fafad94ced7df4f2e5c1ade63b243c04ef02293dff3ffe +size 161 diff --git a/tests/hg19-chr22/Case_1_index.gatk_hc.db-info.tsv-expected b/tests/hg19-chr22/Case_1_index.gatk_hc.db-info.tsv-expected new file mode 100644 index 0000000..9d765e2 --- /dev/null +++ b/tests/hg19-chr22/Case_1_index.gatk_hc.db-info.tsv-expected @@ -0,0 +1,9 @@ +genomebuild db_name release +GRCh37 clinvar for-testing +GRCh37 exac r1.0 +GRCh37 gnomad_exomes r2.1.1 +GRCh37 gnomad_genomes r2.1.1 +GRCh37 hgmd_public for-testing +GRCh37 thousand_genomes v3.20101123 +GRCh37 varfish-annotator 0.26-SNAPSHOT +GRCh37 varfish-annotator-db for-testing diff --git a/tests/hg19-chr22/Case_1_index.gatk_hc.gts.tsv-expected b/tests/hg19-chr22/Case_1_index.gatk_hc.gts.tsv-expected new file mode 100644 index 0000000..98792b5 --- /dev/null +++ b/tests/hg19-chr22/Case_1_index.gatk_hc.gts.tsv-expected @@ -0,0 +1,167 @@ +release chromosome chromosome_no start end bin reference alternative var_type case_id set_id info genotype num_hom_alt num_hom_ref num_het num_hemi_alt num_hemi_ref in_clinvar exac_frequency exac_homozygous exac_heterozygous exac_hemizygous thousand_genomes_frequency thousand_genomes_homozygous thousand_genomes_heterozygous thousand_genomes_hemizygous gnomad_exomes_frequency gnomad_exomes_homozygous gnomad_exomes_heterozygous gnomad_exomes_hemizygous gnomad_genomes_frequency gnomad_genomes_homozygous gnomad_genomes_heterozygous gnomad_genomes_hemizygous refseq_gene_id refseq_transcript_id refseq_transcript_coding refseq_hgvs_c refseq_hgvs_p refseq_effect refseq_exon_dist ensembl_gene_id ensembl_transcript_id ensembl_transcript_coding ensembl_hgvs_c ensembl_hgvs_p ensembl_effect ensembl_exon_dist +GRCh37 22 22 17442987 17442987 718 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":42,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":28,"""dp""":52,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.199719 118 759 0 0 0 0 0 0.164199 494 4157 0 128954 NM_001037814.1 TRUE c.*636G>A p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000215568 ENST00000400588.1 TRUE c.*636G>A p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17443131 17443131 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":54,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":33,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":30,"""dp""":52,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.199117 118 756 0 0 0 0 0 0.164276 497 4160 0 128954 NM_001037814.1 TRUE c.*492A>G p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000215568 ENST00000400588.1 TRUE c.*492A>G p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17443238 17443238 718 T A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":46,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":42,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":25,"""dp""":48,"""gq""":99}} 0 0 3 0 0 FALSE 0 0 0 0 0.547973 750 1230 0 0 0 0 0 0.574144 5255 7494 0 128954 NM_001037814.1 TRUE c.*385A>T p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000215568 ENST00000400588.1 TRUE c.*385A>T p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17444231 17444231 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":45,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":28,"""dp""":43,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":45,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0614211 21 264 0 0 0 0 0 0.0819131 137 2283 0 128954 NM_001037814.1 TRUE c.1581+384A>G p.= {"coding_transcript_intron_variant"} 384 ENSG00000215568 ENST00000400588.1 TRUE c.1581+384A>G p.= {"coding_transcript_intron_variant"} 384 +GRCh37 22 22 17445502 17445502 718 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":33,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":24,"""dp""":46,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":37,"""gq""":99}} 0 0 3 0 0 FALSE 0 0 0 0 0.546166 745 1231 0 0 0 0 0 0.56894 5120 7561 0 128954 NM_001037814.1 TRUE c.1476+154T>G p.= {"coding_transcript_intron_variant"} 154 ENSG00000215568 ENST00000400588.1 TRUE c.1476+154T>G p.= {"coding_transcript_intron_variant"} 154 +GRCh37 22 22 17446715 17446715 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":11,"""dp""":32,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":30,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":39,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0863107 30 370 0 0 0 0 0 0.102647 169 2881 0 128954 NM_001037814.1 TRUE c.1288+275C>T p.= {"coding_transcript_intron_variant"} 275 ENSG00000215568 ENST00000400588.1 TRUE c.1288+275C>T p.= {"coding_transcript_intron_variant"} 275 +GRCh37 22 22 17446906 17446906 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":26,"""dp""":45,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":43,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":41,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0863107 29 372 0 0 0 0 0 0.102198 167 2874 0 128954 NM_001037814.1 TRUE c.1288+84C>T p.= {"coding_transcript_intron_variant"} 84 ENSG00000215568 ENST00000400588.1 TRUE c.1288+84C>T p.= {"coding_transcript_intron_variant"} 84 +GRCh37 22 22 17446914 17446914 718 T G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":47,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":26,"""dp""":43,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":40,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.203934 127 762 0 0 0 0 0 0.172011 549 4298 0 128954 NM_001037814.1 TRUE c.1288+76A>C p.= {"coding_transcript_intron_variant"} 76 ENSG00000215568 ENST00000400588.1 TRUE c.1288+76A>C p.= {"coding_transcript_intron_variant"} 76 +GRCh37 22 22 17446991 17446991 718 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":26,"""dp""":39,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":46,"""dp""":46,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":32,"""dp""":32,"""gq""":96}} 2 0 1 0 0 FALSE 0.772 36326 20475 0 0.825171 1718 675 0 0.777145 76015 41605 0 0.808722 10388 4592 0 128954 NM_001037814.1 TRUE c.1287G>A p.= {"splice_region_variant","synonymous_variant"} 0 ENSG00000215568 ENST00000400588.1 TRUE c.1287G>A p.= {"splice_region_variant","synonymous_variant"} 0 +GRCh37 22 22 17447350 17447350 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":21,"""gq""":63},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":38,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":43,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.00521879 1 24 0 0 0 0 0 0.00850698 1 265 0 128954 NM_001037814.1 TRUE c.1024-96C>T p.= {"coding_transcript_intron_variant"} 96 ENSG00000215568 ENST00000400588.1 TRUE c.1024-96C>T p.= {"coding_transcript_intron_variant"} 96 +GRCh37 22 22 17447438 17447438 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":48,"""dp""":48,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":41,"""dp""":41,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.742272 1375 948 0 0 0 0 0 0.738208 8572 5987 0 128954 NM_001037814.1 TRUE c.1024-184C>T p.= {"coding_transcript_intron_variant"} 184 ENSG00000215568 ENST00000400588.1 TRUE c.1024-184C>T p.= {"coding_transcript_intron_variant"} 184 +GRCh37 22 22 17448143 17448143 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":27,"""dp""":27,"""gq""":81},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":51,"""dp""":51,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.823766 1717 670 0 0 0 0 0 0.807349 10267 4602 0 128954 NM_001037814.1 TRUE c.1024-889C>T p.= {"coding_transcript_intron_variant"} 889 ENSG00000215568 ENST00000400588.1 TRUE c.1024-889C>T p.= {"coding_transcript_intron_variant"} 889 +GRCh37 22 22 17449076 17449076 718 C G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":25,"""dp""":50,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":25,"""dp""":25,"""gq""":75},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":50,"""dp""":50,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.826576 1721 676 0 0 0 0 0 0.809263 10396 4580 0 128954 NM_001037814.1 TRUE c.1023+112G>C p.= {"coding_transcript_intron_variant"} 112 ENSG00000215568 ENST00000400588.1 TRUE c.1023+112G>C p.= {"coding_transcript_intron_variant"} 112 +GRCh37 22 22 17451528 17451528 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":29,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":16,"""gq""":48},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":36,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0301084 3 144 0 0 0 0 0 0.0404552 40 1189 0 128954 NM_001037814.1 TRUE c.687-445C>T p.= {"coding_transcript_intron_variant"} 445 ENSG00000215568 ENST00000400588.1 TRUE c.687-445C>T p.= {"coding_transcript_intron_variant"} 445 +GRCh37 22 22 17451613 17451613 718 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":42,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":25,"""gq""":75},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":35,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0576074 9 269 0 0 0 0 0 0.0939713 135 2676 0 128954 NM_001037814.1 TRUE c.687-530G>A p.= {"coding_transcript_intron_variant"} 530 ENSG00000215568 ENST00000400588.1 TRUE c.687-530G>A p.= {"coding_transcript_intron_variant"} 530 +GRCh37 22 22 17451710 17451710 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":43,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":42,"""gq""":99}} 0 0 3 0 0 FALSE 0 0 0 0 0.135688 59 558 0 0 0 0 0 0.191286 604 4785 0 128954 NM_001037814.1 TRUE c.687-627A>G p.= {"coding_transcript_intron_variant"} 627 ENSG00000215568 ENST00000400588.1 TRUE c.687-627A>G p.= {"coding_transcript_intron_variant"} 627 +GRCh37 22 22 17451854 17451854 718 G C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":47,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":12,"""dp""":34,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":42,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.155761 120 536 0 0 0 0 0 0.161126 550 3931 0 128954 NM_001037814.1 TRUE c.687-771C>G p.= {"coding_transcript_intron_variant"} 771 ENSG00000215568 ENST00000400588.1 TRUE c.687-771C>G p.= {"coding_transcript_intron_variant"} 771 +GRCh37 22 22 17451883 17451883 718 C A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":41,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":29,"""gq""":87},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":34,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0600161 9 281 0 0 0 0 0 0.0942456 135 2642 0 128954 NM_001037814.1 TRUE c.687-800G>T p.= {"coding_transcript_intron_variant"} 800 ENSG00000215568 ENST00000400588.1 TRUE c.687-800G>T p.= {"coding_transcript_intron_variant"} 800 +GRCh37 22 22 17452300 17452300 718 T G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":44,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":12,"""dp""":26,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":1,"""dp""":41,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0666399 21 290 0 0 0 0 0 0.0901733 160 2510 0 128954 NM_001037814.1 TRUE c.687-1217A>C p.= {"coding_transcript_intron_variant"} 1217 ENSG00000215568 ENST00000400588.1 TRUE c.687-1217A>C p.= {"coding_transcript_intron_variant"} 1217 +GRCh37 22 22 17452925 17452925 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":25,"""dp""":46,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":36,"""dp""":36,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":54,"""dp""":54,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.816339 1681 705 0 0 0 0 0 0.792801 10023 4821 0 128954 NM_001037814.1 TRUE c.687-1842C>T p.= {"coding_transcript_intron_variant"} 1842 ENSG00000215568 ENST00000400588.1 TRUE c.687-1842C>T p.= {"coding_transcript_intron_variant"} 1842 +GRCh37 22 22 17452966 17452966 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":41,"""dp""":41,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":35,"""dp""":35,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":45,"""dp""":45,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.848254 1814 598 0 0 0 0 0 0.834035 11024 4119 0 128954 NM_001037814.1 TRUE c.687-1883A>G p.= {"coding_transcript_intron_variant"} 1883 ENSG00000215568 ENST00000400588.1 TRUE c.687-1883A>G p.= {"coding_transcript_intron_variant"} 1883 +GRCh37 22 22 17453588 17453588 718 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":36,"""dp""":36,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":39,"""dp""":39,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.685468 1177 1061 0 0 0 0 0 0.672935 7102 6836 0 128954 NM_001037814.1 TRUE c.687-2505T>G p.= {"coding_transcript_intron_variant"} 2505 ENSG00000215568 ENST00000400588.1 TRUE c.687-2505T>G p.= {"coding_transcript_intron_variant"} 2505 +GRCh37 22 22 17453844 17453844 718 A T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":24,"""gq""":72},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":28,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":41,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.205339 132 759 0 0 0 0 0 0.164773 524 4114 0 128954 NM_001037814.1 TRUE c.687-2761T>A p.= {"coding_transcript_intron_variant"} 2761 ENSG00000215568 ENST00000400588.1 TRUE c.687-2761T>A p.= {"coding_transcript_intron_variant"} 2761 +GRCh37 22 22 17453902 17453902 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":30,"""gq""":90},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":34,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":44,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0612204 11 283 0 0 0 0 0 0.0930292 133 2654 0 128954 NM_001037814.1 TRUE c.687-2819C>T p.= {"coding_transcript_intron_variant"} 2819 ENSG00000215568 ENST00000400588.1 TRUE c.687-2819C>T p.= {"coding_transcript_intron_variant"} 2819 +GRCh37 22 22 17454486 17454486 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":41,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":11,"""dp""":20,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":25,"""dp""":51,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.229627 171 802 0 0 0 0 0 0.184175 671 4433 0 128954 NM_001037814.1 TRUE c.687-3403A>G p.= {"coding_transcript_intron_variant"} 3403 ENSG00000215568 ENST00000400588.1 TRUE c.687-3403A>G p.= {"coding_transcript_intron_variant"} 3403 +GRCh37 22 22 17454695 17454695 718 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":30,"""gq""":90},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":12,"""dp""":24,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":34,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.204737 132 756 0 0 0 0 0 0.164029 516 4108 0 128954 NM_001037814.1 TRUE c.687-3612G>A p.= {"coding_transcript_intron_variant"} 3612 ENSG00000215568 ENST00000400588.1 TRUE c.687-3612G>A p.= {"coding_transcript_intron_variant"} 3612 +GRCh37 22 22 17454945 17454945 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":44,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":27,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":24,"""dp""":41,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.20554 134 756 0 0 0 0 0 0.164201 518 4114 0 128954 NM_001037814.1 TRUE c.687-3862C>T p.= {"coding_transcript_intron_variant"} 3862 ENSG00000215568 ENST00000400588.1 TRUE c.687-3862C>T p.= {"coding_transcript_intron_variant"} 3862 +GRCh37 22 22 17455630 17455630 718 C A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":30,"""dp""":46,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":33,"""dp""":33,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":47,"""dp""":47,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.823766 1712 680 0 0 0 0 0 0.804978 10302 4624 0 128954 NM_001037814.1 TRUE c.687-4547G>T p.= {"coding_transcript_intron_variant"} 4547 ENSG00000215568 ENST00000400588.1 TRUE c.687-4547G>T p.= {"coding_transcript_intron_variant"} 4547 +GRCh37 22 22 17455735 17455735 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":30,"""gq""":90},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":32,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":38,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.205339 132 759 0 0 0 0 0 0.164699 522 4117 0 128954 NM_001037814.1 TRUE c.687-4652C>T p.= {"coding_transcript_intron_variant"} 4652 ENSG00000215568 ENST00000400588.1 TRUE c.687-4652C>T p.= {"coding_transcript_intron_variant"} 4652 +GRCh37 22 22 17456370 17456370 718 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":49,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":41,"""dp""":41,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":48,"""dp""":48,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.825773 1719 676 0 0 0 0 0 0.804933 10307 4611 0 128954 NM_001037814.1 TRUE c.687-5287T>C p.= {"coding_transcript_intron_variant"} 5287 ENSG00000215568 ENST00000400588.1 TRUE c.687-5287T>C p.= {"coding_transcript_intron_variant"} 5287 +GRCh37 22 22 17456642 17456642 718 C A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":36,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":43,"""dp""":44,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":49,"""dp""":49,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.79988 1623 739 0 0 0 0 0 0.78203 9715 5010 0 128954 NM_001037814.1 TRUE c.687-5559G>T p.= {"coding_transcript_intron_variant"} 5559 ENSG00000215568 ENST00000400588.1 TRUE c.687-5559G>T p.= {"coding_transcript_intron_variant"} 5559 +GRCh37 22 22 17456879 17456879 718 C CA indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":11,"""dp""":28,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":39,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":44,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0977519 38 411 0 0 0 0 0 0.117852 203 3110 0 128954 NM_001037814.1 TRUE c.687-5797_687-5796insT p.= {"coding_transcript_intron_variant"} 5796 ENSG00000215568 ENST00000400588.1 TRUE c.687-5797_687-5796insT p.= {"coding_transcript_intron_variant"} 5796 +GRCh37 22 22 17457136 17457136 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":34,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":33,"""dp""":33,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":49,"""dp""":49,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.825773 1719 676 0 0 0 0 0 0.805407 10312 4611 0 128954 NM_001037814.1 TRUE c.687-6053A>G p.= {"coding_transcript_intron_variant"} 6053 ENSG00000215568 ENST00000400588.1 TRUE c.687-6053A>G p.= {"coding_transcript_intron_variant"} 6053 +GRCh37 22 22 17457276 17457276 718 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":40,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":27,"""dp""":27,"""gq""":81},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":39,"""dp""":39,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.825974 1720 675 0 0 0 0 0 0.80503 10320 4617 0 128954 NM_001037814.1 TRUE c.687-6193G>A p.= {"coding_transcript_intron_variant"} 6193 ENSG00000215568 ENST00000400588.1 TRUE c.687-6193G>A p.= {"coding_transcript_intron_variant"} 6193 +GRCh37 22 22 17457761 17457761 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":49,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":41,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":40,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0640305 12 295 0 0 0 0 0 0.0946325 141 2687 0 128954 NM_001037814.1 TRUE c.687-6678A>G p.= {"coding_transcript_intron_variant"} 6678 ENSG00000215568 ENST00000400588.1 TRUE c.687-6678A>G p.= {"coding_transcript_intron_variant"} 6678 +GRCh37 22 22 17457979 17457979 718 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":12,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":30,"""dp""":30,"""gq""":90},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":33,"""dp""":33,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.826174 1720 676 0 0 0 0 0 0.805329 10318 4603 0 128954 NM_001037814.1 TRUE c.687-6896T>C p.= {"coding_transcript_intron_variant"} 6896 ENSG00000215568 ENST00000400588.1 TRUE c.687-6896T>C p.= {"coding_transcript_intron_variant"} 6896 +GRCh37 22 22 17458083 17458083 718 G T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":31,"""gq""":93},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":30,"""gq""":90},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":28,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0634283 12 292 0 0 0 0 0 0.0941345 138 2677 0 128954 NM_001037814.1 TRUE c.687-7000C>A p.= {"coding_transcript_intron_variant"} 7000 ENSG00000215568 ENST00000400588.1 TRUE c.687-7000C>A p.= {"coding_transcript_intron_variant"} 7000 +GRCh37 22 22 17458238 17458238 718 C CAA indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":40,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":9,"""dp""":19,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":32,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.140305 26 647 0 0 0 0 0 0.222272 375 3186 0 128954 NM_001037814.1 TRUE c.687-7156_687-7155insTT p.= {"coding_transcript_intron_variant"} 7155 ENSG00000215568 ENST00000400588.1 TRUE c.687-7156_687-7155insTT p.= {"coding_transcript_intron_variant"} 7155 +GRCh37 22 22 17458882 17458882 718 A AGACAC indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":36,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":31,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":38,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.491369 594 1260 0 0 0 0 0 0.485924 3708 7739 0 128954 NM_001037814.1 TRUE c.687-7800_687-7799insGTGTC p.= {"coding_transcript_intron_variant"} 7799 ENSG00000215568 ENST00000400588.1 TRUE c.687-7800_687-7799insGTGTC p.= {"coding_transcript_intron_variant"} 7799 +GRCh37 22 22 17458962 17458963 718 GA G indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":40,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":32,"""dp""":32,"""gq""":96},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":40,"""dp""":40,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.800482 1623 742 0 0 0 0 0 0.781987 9732 5020 0 128954 NM_001037814.1 TRUE c.687-7880del p.= {"coding_transcript_intron_variant"} 7879 ENSG00000215568 ENST00000400588.1 TRUE c.687-7880del p.= {"coding_transcript_intron_variant"} 7879 +GRCh37 22 22 17459768 17459768 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":32,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":28,"""gq""":84}} 0 1 2 0 0 FALSE 0 0 0 0 0.0600161 20 259 0 0 0 0 0 0.0872682 162 2415 0 128954 NM_001037814.1 TRUE c.687-8685A>G p.= {"coding_transcript_intron_variant"} 8685 ENSG00000215568 ENST00000400588.1 TRUE c.687-8685A>G p.= {"coding_transcript_intron_variant"} 8685 +GRCh37 22 22 17460357 17460357 718 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":53,"""dp""":53,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":35,"""dp""":35,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":29,"""dp""":29,"""gq""":87}} 3 0 0 0 0 FALSE 0 0 0 0 1.0 2491 0 0 0 0 0 0 0.999873 15689 4 0 128954 NM_001037814.1 TRUE c.686+8493T>C p.= {"coding_transcript_intron_variant"} 8493 ENSG00000215568 ENST00000400588.1 TRUE c.686+8493T>C p.= {"coding_transcript_intron_variant"} 8493 +GRCh37 22 22 17461883 17461883 718 A T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":35,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":21,"""gq""":61}} 0 1 2 0 0 FALSE 0 0 0 0 0.03332 9 148 0 0 0 0 0 0.0641271 92 1826 0 128954 NM_001037814.1 TRUE c.686+6967T>A p.= {"coding_transcript_intron_variant"} 6967 ENSG00000215568 ENST00000400588.1 TRUE c.686+6967T>A p.= {"coding_transcript_intron_variant"} 6967 +GRCh37 22 22 17462185 17462185 718 C A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":23,"""dp""":42,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":28,"""dp""":28,"""gq""":84},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":34,"""dp""":34,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.812124 1673 700 0 0 0 0 0 0.768057 9213 4989 0 128954 NM_001037814.1 TRUE c.686+6665G>T p.= {"coding_transcript_intron_variant"} 6665 ENSG00000215568 ENST00000400588.1 TRUE c.686+6665G>T p.= {"coding_transcript_intron_variant"} 6665 +GRCh37 22 22 17463189 17463189 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":26,"""dp""":48,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":12,"""dp""":25,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":57,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0953432 41 393 0 0 0 0 0 0.115546 224 3176 0 128954 NM_001037814.1 TRUE c.686+5661A>G p.= {"coding_transcript_intron_variant"} 5661 ENSG00000215568 ENST00000400588.1 TRUE c.686+5661A>G p.= {"coding_transcript_intron_variant"} 5661 +GRCh37 22 22 17463620 17463620 718 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":24,"""dp""":54,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":39,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":2,"""dp""":33,"""gq""":78}} 0 1 2 0 0 FALSE 0 0 0 0 0.0951425 40 394 0 0 0 0 0 0.115497 223 3179 0 128954 NM_001037814.1 TRUE c.686+5230T>G p.= {"coding_transcript_intron_variant"} 5230 ENSG00000215568 ENST00000400588.1 TRUE c.686+5230T>G p.= {"coding_transcript_intron_variant"} 5230 +GRCh37 22 22 17467411 17467411 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":37,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":39,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0648334 11 301 0 0 0 0 0 0.0956796 146 2711 0 128954 NM_001037814.1 TRUE c.686+1439C>T p.= {"coding_transcript_intron_variant"} 1439 ENSG00000215568 ENST00000400588.1 TRUE c.686+1439C>T p.= {"coding_transcript_intron_variant"} 1439 +GRCh37 22 22 17467474 17467474 718 C A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":28,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":43,"""dp""":43,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":42,"""dp""":42,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.823966 1711 683 0 0 0 0 0 0.805167 10309 4624 0 128954 NM_001037814.1 TRUE c.686+1376G>T p.= {"coding_transcript_intron_variant"} 1376 ENSG00000215568 ENST00000400588.1 TRUE c.686+1376G>T p.= {"coding_transcript_intron_variant"} 1376 +GRCh37 22 22 17467684 17467684 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":38,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":35,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0642312 11 298 0 0 0 0 0 0.0956491 144 2715 0 128954 NM_001037814.1 TRUE c.686+1166C>T p.= {"coding_transcript_intron_variant"} 1166 ENSG00000215568 ENST00000400588.1 TRUE c.686+1166C>T p.= {"coding_transcript_intron_variant"} 1166 +GRCh37 22 22 17469664 17469664 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":37,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":38,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":42,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0638298 11 296 0 0 0 0 0 0.0954415 144 2706 0 128954 NM_001037814.1 TRUE c.479-607C>T p.= {"coding_transcript_intron_variant"} 607 ENSG00000215568 ENST00000400588.1 TRUE c.479-607C>T p.= {"coding_transcript_intron_variant"} 607 +GRCh37 22 22 17470779 17470779 718 C A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":42,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":24,"""dp""":42,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":26,"""dp""":45,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.160779 89 623 0 0 0 0 0 0.134506 362 3496 0 128954 NM_001037814.1 TRUE c.479-1722G>T p.= {"coding_transcript_intron_variant"} 1722 ENSG00000215568 ENST00000400588.1 TRUE c.479-1722G>T p.= {"coding_transcript_intron_variant"} 1722 +GRCh37 22 22 17471354 17471354 718 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":39,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":33,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":23,"""dp""":38,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.20012 125 747 0 0 0 0 0 0.161509 504 4054 0 128954 NM_001037814.1 TRUE c.478+1409G>A p.= {"coding_transcript_intron_variant"} 1409 ENSG00000215568 ENST00000400588.1 TRUE c.478+1409G>A p.= {"coding_transcript_intron_variant"} 1409 +GRCh37 22 22 17471886 17471887 718 AT A indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":40,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":39,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":41,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0164593 0 82 0 0 0 0 0 0.0236654 16 711 0 128954 NM_001037814.1 TRUE c.478+876del p.= {"coding_transcript_intron_variant"} 876 ENSG00000215568 ENST00000400588.1 TRUE c.478+876del p.= {"coding_transcript_intron_variant"} 876 +GRCh37 22 22 17472071 17472071 718 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":36,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":25,"""dp""":25,"""gq""":75},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":39,"""dp""":39,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.825974 1719 677 0 0 0 0 0 0.805879 10261 4565 0 128954 NM_001037814.1 TRUE c.478+692T>C p.= {"coding_transcript_intron_variant"} 692 ENSG00000215568 ENST00000400588.1 TRUE c.478+692T>C p.= {"coding_transcript_intron_variant"} 692 +GRCh37 22 22 17472134 17472134 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":31,"""gq""":92},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":29,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":34,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.00722601 2 32 0 0 0 0 0 0.0160254 6 487 0 128954 NM_001037814.1 TRUE c.478+629A>G p.= {"coding_transcript_intron_variant"} 629 ENSG00000215568 ENST00000400588.1 TRUE c.478+629A>G p.= {"coding_transcript_intron_variant"} 629 +GRCh37 22 22 17473888 17473888 718 G C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":29,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":39,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0949418 39 395 0 0 0 0 0 0.115083 221 3167 0 128954 NM_001037814.1 TRUE c.175-822C>G p.= {"coding_transcript_intron_variant"} 822 ENSG00000215568 ENST00000400588.1 TRUE c.175-822C>G p.= {"coding_transcript_intron_variant"} 822 +GRCh37 22 22 17474812 17474812 718 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":45,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":37,"""dp""":37,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":32,"""dp""":32,"""gq""":96}} 2 0 1 0 0 FALSE 0 0 0 0 0.828382 1727 673 0 0 0 0 0 0.805875 10319 4602 0 128954 NM_001037814.1 TRUE c.175-1746T>C p.= {"coding_transcript_intron_variant"} 1746 ENSG00000215568 ENST00000400588.1 TRUE c.175-1746T>C p.= {"coding_transcript_intron_variant"} 1746 +GRCh37 22 22 17475921 17475921 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":58,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":25,"""dp""":50,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":37,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.180851 112 677 0 0 0 0 0 0.145361 413 3736 0 128954 NM_001037814.1 TRUE c.175-2855A>G p.= {"coding_transcript_intron_variant"} 2855 ENSG00000215568 ENST00000400588.1 TRUE c.175-2855A>G p.= {"coding_transcript_intron_variant"} 2855 +GRCh37 22 22 17476064 17476064 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":37,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":24,"""gq""":72},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":11,"""dp""":25,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0662385 13 304 0 0 0 0 0 0.097379 147 2760 0 128954 NM_001037814.1 TRUE c.175-2998A>G p.= {"coding_transcript_intron_variant"} 2998 ENSG00000215568 ENST00000400588.1 TRUE c.175-2998A>G p.= {"coding_transcript_intron_variant"} 2998 +GRCh37 22 22 17476702 17476702 718 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":48,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":31,"""gq""":93},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":31,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0660377 13 303 0 0 0 0 0 0.0973993 149 2758 0 128954 NM_001037814.1 TRUE c.175-3636T>G p.= {"coding_transcript_intron_variant"} 3636 ENSG00000215568 ENST00000400588.1 TRUE c.175-3636T>G p.= {"coding_transcript_intron_variant"} 3636 +GRCh37 22 22 17477589 17477589 718 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":28,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":17,"""dp""":17,"""gq""":51},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":29,"""dp""":44,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.334404 325 1016 0 0 0 0 0 0.307032 1598 6419 0 128954 NM_001037814.1 TRUE c.175-4523T>C p.= {"coding_transcript_intron_variant"} 4523 ENSG00000215568 ENST00000400588.1 TRUE c.175-4523T>C p.= {"coding_transcript_intron_variant"} 4523 +GRCh37 22 22 17477688 17477688 718 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":16,"""dp""":16,"""gq""":48},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":7,"""dp""":7,"""gq""":24},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":7,"""dp""":7,"""gq""":21}} 3 0 0 0 0 FALSE 0 0 0 0 1.0 2491 0 0 0 0 0 0 1.0 15381 0 0 128954 NM_001037814.1 TRUE c.175-4622T>G p.= {"coding_transcript_intron_variant"} 4622 ENSG00000215568 ENST00000400588.1 TRUE c.175-4622T>G p.= {"coding_transcript_intron_variant"} 4622 +GRCh37 22 22 17477706 17477706 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":5,"""dp""":15,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":10,"""dp""":10,"""gq""":30},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":8,"""dp""":8,"""gq""":24}} 2 0 1 0 0 FALSE 0 0 0 0 0.826174 1719 678 0 0 0 0 0 0.795531 7640 3730 0 128954 NM_001037814.1 TRUE c.175-4640A>G p.= {"coding_transcript_intron_variant"} 4640 ENSG00000215568 ENST00000400588.1 TRUE c.175-4640A>G p.= {"coding_transcript_intron_variant"} 4640 +GRCh37 22 22 17477859 17477859 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":33,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":20,"""gq""":60},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":22,"""gq""":66}} 0 2 1 0 0 FALSE 0 0 0 0 0.0250903 4 117 0 0 0 0 0 0.0364175 38 1067 0 128954 NM_001037814.1 TRUE c.175-4793A>G p.= {"coding_transcript_intron_variant"} 4793 ENSG00000215568 ENST00000400588.1 TRUE c.175-4793A>G p.= {"coding_transcript_intron_variant"} 4793 +GRCh37 22 22 17478236 17478236 718 T A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":48,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":12,"""dp""":29,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":46,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0018065 0 9 0 0 0 0 0 0.00764283 0 240 0 128954 NM_001037814.1 TRUE c.175-5170A>T p.= {"coding_transcript_intron_variant"} 5170 ENSG00000215568 ENST00000400588.1 TRUE c.175-5170A>T p.= {"coding_transcript_intron_variant"} 5170 +GRCh37 22 22 17478728 17478728 718 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":43,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":31,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":49,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0592132 20 255 0 0 0 0 0 0.0866046 162 2394 0 128954 NM_001037814.1 TRUE c.175-5662C>T p.= {"coding_transcript_intron_variant"} 5662 ENSG00000215568 ENST00000400588.1 TRUE c.175-5662C>T p.= {"coding_transcript_intron_variant"} 5662 +GRCh37 22 22 17479400 17479400 718 G T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":1,"""dp""":42,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":28,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":28,"""dp""":51,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.200723 126 748 0 0 0 0 0 0.161319 504 4050 0 128954 NM_001037814.1 TRUE c.175-6334C>A p.= {"coding_transcript_intron_variant"} 6334 ENSG00000215568 ENST00000400588.1 TRUE c.175-6334C>A p.= {"coding_transcript_intron_variant"} 6334 +GRCh37 22 22 17480064 17480064 718 T A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":28,"""gq""":84},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":37,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0656363 13 301 0 0 0 0 0 0.0961771 143 2733 0 128954 NM_001037814.1 TRUE c.175-6998A>T p.= {"coding_transcript_intron_variant"} 6998 ENSG00000215568 ENST00000400588.1 TRUE c.175-6998A>T p.= {"coding_transcript_intron_variant"} 6998 +GRCh37 22 22 17481048 17481048 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":42,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":32,"""dp""":32,"""gq""":96},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":47,"""dp""":47,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.824769 1711 687 0 0 0 0 0 0.804312 10289 4642 0 128954 NM_001037814.1 TRUE c.174+7783A>G p.= {"coding_transcript_intron_variant"} 7783 ENSG00000215568 ENST00000400588.1 TRUE c.174+7783A>G p.= {"coding_transcript_intron_variant"} 7783 +GRCh37 22 22 17481355 17481355 718 C CT indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":10,"""dp""":24,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":38,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0650341 21 282 0 0 0 0 0 0.0867961 141 2400 0 128954 NM_001037814.1 TRUE c.174+7475_174+7476insA p.= {"coding_transcript_intron_variant"} 7476 ENSG00000215568 ENST00000400588.1 TRUE c.174+7475_174+7476insA p.= {"coding_transcript_intron_variant"} 7476 +GRCh37 22 22 17482086 17482086 718 G T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":47,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":37,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":23,"""dp""":42,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0620233 11 287 0 0 0 0 0 0.0942121 140 2676 0 128954 NM_001037814.1 TRUE c.174+6745C>A p.= {"coding_transcript_intron_variant"} 6745 ENSG00000215568 ENST00000400588.1 TRUE c.174+6745C>A p.= {"coding_transcript_intron_variant"} 6745 +GRCh37 22 22 17482227 17482227 718 T TC indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":37,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":33,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":25,"""gq""":75}} 0 2 1 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 3.18492E-5 0 1 0 128954 NM_001037814.1 TRUE c.174+6603_174+6604insG p.= {"coding_transcript_intron_variant"} 6604 ENSG00000215568 ENST00000400588.1 TRUE c.174+6603_174+6604insG p.= {"coding_transcript_intron_variant"} 6604 +GRCh37 22 22 17482825 17482825 718 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":39,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":35,"""dp""":35,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":47,"""dp""":47,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.825773 1719 676 0 0 0 0 0 0.806073 10334 4604 0 128954 NM_001037814.1 TRUE c.174+6006T>C p.= {"coding_transcript_intron_variant"} 6006 ENSG00000215568 ENST00000400588.1 TRUE c.174+6006T>C p.= {"coding_transcript_intron_variant"} 6006 +GRCh37 22 22 17482847 17482847 718 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":40,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":36,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":27,"""dp""":48,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.160177 88 622 0 0 0 0 0 0.134098 356 3496 0 128954 NM_001037814.1 TRUE c.174+5984G>A p.= {"coding_transcript_intron_variant"} 5984 ENSG00000215568 ENST00000400588.1 TRUE c.174+5984G>A p.= {"coding_transcript_intron_variant"} 5984 +GRCh37 22 22 17483804 17483805 718 AG A indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":44,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":32,"""gq""":96},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":12,"""dp""":34,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0636291 12 293 0 0 0 0 0 0.0944232 138 2687 0 128954 NM_001037814.1 TRUE c.174+5026del p.= {"coding_transcript_intron_variant"} 5026 ENSG00000215568 ENST00000400588.1 TRUE c.174+5026del p.= {"coding_transcript_intron_variant"} 5026 +GRCh37 22 22 17484650 17484650 718 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":40,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":32,"""gq""":96},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":34,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.0664392 15 301 0 0 0 0 0 0.0973152 143 2766 0 128954 NM_001037814.1 TRUE c.174+4181T>G p.= {"coding_transcript_intron_variant"} 4181 ENSG00000215568 ENST00000400588.1 TRUE c.174+4181T>G p.= {"coding_transcript_intron_variant"} 4181 +GRCh37 22 22 17484733 17484733 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":34,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":31,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":38,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.0116419 2 54 0 0 0 0 0 0.0227854 13 687 0 128954 NM_001037814.1 TRUE c.174+4098A>G p.= {"coding_transcript_intron_variant"} 4098 ENSG00000215568 ENST00000400588.1 TRUE c.174+4098A>G p.= {"coding_transcript_intron_variant"} 4098 +GRCh37 22 22 17486937 17486937 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":30,"""gq""":90},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":43,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":36,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.068045 15 309 0 0 0 0 0 0.0973612 145 2765 0 128954 NM_001037814.1 TRUE c.174+1894A>G p.= {"coding_transcript_intron_variant"} 1894 ENSG00000215568 ENST00000400588.1 TRUE c.174+1894A>G p.= {"coding_transcript_intron_variant"} 1894 +GRCh37 22 22 17488430 17488430 718 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":31,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":37,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":30,"""gq""":89}} 0 1 2 0 0 FALSE 0 0 0 0 0.0796869 27 343 0 0 0 0 0 0.102473 176 2731 0 128954 NM_001037814.1 TRUE c.174+401A>G p.= {"coding_transcript_intron_variant"} 401 ENSG00000215568 ENST00000400588.1 TRUE c.174+401A>G p.= {"coding_transcript_intron_variant"} 401 +GRCh37 22 22 17488669 17488669 718 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":36,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":40,"""dp""":40,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":45,"""dp""":45,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.809314 1639 754 0 0 0 0 0 0.794817 9984 4905 0 128954 NM_001037814.1 TRUE c.174+162G>A p.= {"coding_transcript_intron_variant"} 162 ENSG00000215568 ENST00000400588.1 TRUE c.174+162G>A p.= {"coding_transcript_intron_variant"} 162 +GRCh37 22 22 17488727 17488727 718 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":37,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":43,"""dp""":43,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":50,"""dp""":50,"""gq""":99}} 2 0 1 0 0 FALSE 0 0 0 0 0.813328 1653 746 0 0 0 0 0 0.796328 10009 4880 0 128954 NM_001037814.1 TRUE c.174+104T>G p.= {"coding_transcript_intron_variant"} 104 ENSG00000215568 ENST00000400588.1 TRUE c.174+104T>G p.= {"coding_transcript_intron_variant"} 104 +GRCh37 22 22 17488823 17488823 718 C CG indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":38,"""dp""":38,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":49,"""dp""":49,"""gq""":99}} 2 0 1 0 0 FALSE 0.783 32903 17465 0 0.8334 1750 652 0 0.794509 72468 35945 0 0.832189 10914 4108 0 128954 NM_001037814.1 TRUE c.174+7_174+8insC p.? {"splice_region_variant","coding_transcript_intron_variant"} 8 ENSG00000215568 ENST00000400588.1 TRUE c.174+7_174+8insC p.? {"splice_region_variant","coding_transcript_intron_variant"} 8 +GRCh37 22 22 17660303 17660303 719 A T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":37,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":26,"""gq""":78},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":36,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.293456 209 1044 0 0 0 0 0 0.350284 1934 7112 0 51816 NM_017424.2 TRUE c.*2070T>A p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*2070T>A p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17660501 17660501 719 C G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":36,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":30,"""gq""":90},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":36,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.581092 930 1035 0 0 0 0 0 0.626397 6408 6804 0 51816 NM_017424.2 TRUE c.*1872G>C p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*1872G>C p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17660556 17660556 719 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":26,"""gq""":78},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":26,"""dp""":41,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.234243 174 819 0 0 0 0 0 0.294155 1465 6260 0 51816 NM_017424.2 TRUE c.*1817A>G p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*1817A>G p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17660646 17660646 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":39,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":27,"""gq""":81},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":23,"""dp""":42,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.282417 205 997 0 0 0 0 0 0.30896 1520 6636 0 51816 NM_017424.2 TRUE c.*1727T>C p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*1727T>C p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17661178 17661178 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":23,"""dp""":41,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":36,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":41,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.335006 311 1047 0 0 0 0 0 0.36062 2174 6943 0 51816 NM_017424.2 TRUE c.*1195T>C p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*1195T>C p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17661347 17661347 719 C G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":27,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":22,"""gq""":66},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":30,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.173023 93 676 0 0 0 0 0 0.241923 974 5630 0 51816 NM_017424.2 TRUE c.*1026G>C p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*1026G>C p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17661764 17661764 719 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":36,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":27,"""gq""":81},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":34,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.228824 152 836 0 0 0 0 0 0.314218 1612 6628 0 51816 NM_017424.2 TRUE c.*609A>G p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*609A>G p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17661791 17661791 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":33,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":29,"""gq""":87},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":32,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.172822 93 675 0 0 0 0 0 0.241588 975 5618 0 51816 NM_017424.2 TRUE c.*582G>A p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*582G>A p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17661922 17661922 719 C G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":25,"""dp""":46,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":43,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":41,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.290044 265 915 0 0 0 0 0 0.364383 2175 7053 0 51816 NM_017424.2 TRUE c.*451G>C p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*451G>C p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17661935 17661935 719 A T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":27,"""dp""":49,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":42,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":43,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.170213 92 664 0 0 0 0 0 0.239793 959 5600 0 51816 NM_017424.2 TRUE c.*438T>A p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*438T>A p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17662163 17662163 719 C G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":44,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":32,"""gq""":96},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":27,"""dp""":50,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.564231 851 1109 0 0 0 0 0 0.606041 5919 7142 0 51816 NM_017424.2 TRUE c.*210G>C p.= {"3_prime_UTR_exon_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.*210G>C p.= {"3_prime_UTR_exon_variant"} 0 +GRCh37 22 22 17662591 17662591 719 C G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":39,"""dp""":39,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":40,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":30,"""dp""":53,"""gq""":99}} 1 0 2 0 0 TRUE 0 0 0 0 0.186672 116 698 0 0 0 0 0 0.275653 1281 6072 0 51816 NM_017424.2 TRUE c.1442+119G>C p.= {"coding_transcript_intron_variant"} 119 ENSG00000093072 ENST00000262607.3 TRUE c.1442+119G>C p.= {"coding_transcript_intron_variant"} 119 +GRCh37 22 22 17662679 17662679 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":49,"""dp""":49,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":27,"""dp""":44,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":28,"""dp""":53,"""gq""":99}} 1 0 2 0 0 TRUE 0.249 4266 21428 0 0.187073 116 700 0 0.246776 8757 43681 0 0.276069 1292 6068 0 51816 NM_017424.2 TRUE c.1442+31G>A p.= {"coding_transcript_intron_variant"} 31 ENSG00000093072 ENST00000262607.3 TRUE c.1442+31G>A p.= {"coding_transcript_intron_variant"} 31 +GRCh37 22 22 17662699 17662699 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":42,"""dp""":42,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":23,"""dp""":38,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":28,"""dp""":54,"""gq""":99}} 1 0 2 0 0 TRUE 0.256 4594 21824 0 0.187073 112 708 0 0.255625 9560 44934 0 0.281751 1332 6161 0 51816 NM_017424.2 TRUE c.1442+11T>C p.= {"coding_transcript_intron_variant"} 11 ENSG00000093072 ENST00000262607.3 TRUE c.1442+11T>C p.= {"coding_transcript_intron_variant"} 11 +GRCh37 22 22 17662793 17662793 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":34,"""dp""":34,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":24,"""dp""":42,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":42,"""gq""":99}} 1 0 2 0 0 TRUE 0.256 4612 21901 0 0.19169 116 723 0 0.255784 9566 45173 0 0.285112 1360 6212 0 51816 NM_017424.2 TRUE c.1359T>C p.= {"synonymous_variant"} 0 ENSG00000093072 ENST00000262607.3 TRUE c.1359T>C p.= {"synonymous_variant"} 0 +GRCh37 22 22 17662917 17662917 719 G C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":35,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":30,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":40,"""gq""":99}} 1 0 2 0 0 TRUE 0.248 4256 21433 0 0.18607 113 701 0 0.246352 8773 43839 0 0.274796 1272 6056 0 51816 NM_017424.2 TRUE c.1240-5C>G p.? {"splice_region_variant","coding_transcript_intron_variant"} 5 ENSG00000093072 ENST00000262607.3 TRUE c.1240-5C>G p.? {"splice_region_variant","coding_transcript_intron_variant"} 5 +GRCh37 22 22 17663117 17663117 719 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":35,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":30,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":37,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.192694 116 728 0 0 0 0 0 0.283339 1327 6206 0 51816 NM_017424.2 TRUE c.1240-205A>G p.= {"coding_transcript_intron_variant"} 205 ENSG00000093072 ENST00000262607.3 TRUE c.1240-205A>G p.= {"coding_transcript_intron_variant"} 205 +GRCh37 22 22 17663127 17663127 719 G T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":34,"""dp""":34,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":28,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":40,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.475713 674 1022 0 0 0 0 0 0.553134 5025 7231 0 51816 NM_017424.2 TRUE c.1240-215C>A p.= {"coding_transcript_intron_variant"} 215 ENSG00000093072 ENST00000262607.3 TRUE c.1240-215C>A p.= {"coding_transcript_intron_variant"} 215 +GRCh37 22 22 17664296 17664296 719 C G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":31,"""dp""":31,"""gq""":93},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":29,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":26,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.194701 119 732 0 0 0 0 0 0.286257 1320 6179 0 51816 NM_017424.2 TRUE c.1082-645G>C p.= {"coding_transcript_intron_variant"} 645 ENSG00000093072 ENST00000262607.3 TRUE c.1082-645G>C p.= {"coding_transcript_intron_variant"} 645 +GRCh37 22 22 17664307 17664307 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":30,"""dp""":30,"""gq""":90},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":12,"""dp""":26,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":10,"""dp""":23,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.191088 118 716 0 0 0 0 0 0.278172 1254 6043 0 51816 NM_017424.2 TRUE c.1082-656G>A p.= {"coding_transcript_intron_variant"} 656 ENSG00000093072 ENST00000262607.3 TRUE c.1082-656G>A p.= {"coding_transcript_intron_variant"} 656 +GRCh37 22 22 17664346 17664346 719 C CT indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":11,"""dp""":11,"""gq""":32},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":4,"""dp""":10,"""gq""":41},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":7,"""dp""":12,"""gq""":63}} 1 0 2 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0.248015 618 2262 0 51816 NM_017424.2 TRUE c.1082-696_1082-695insA p.= {"coding_transcript_intron_variant"} 695 ENSG00000093072 ENST00000262607.3 TRUE c.1082-696_1082-695insA p.= {"coding_transcript_intron_variant"} 695 +GRCh37 22 22 17664556 17664556 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":50,"""dp""":50,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":24,"""dp""":24,"""gq""":72},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":33,"""dp""":33,"""gq""":99}} 3 0 0 0 0 TRUE 0 0 0 0 0.877358 1938 495 0 0 0 0 0 0.88613 12103 3163 0 51816 NM_017424.2 TRUE c.1082-905G>A p.= {"coding_transcript_intron_variant"} 905 ENSG00000093072 ENST00000262607.3 TRUE c.1082-905G>A p.= {"coding_transcript_intron_variant"} 905 +GRCh37 22 22 17664788 17664788 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":32,"""dp""":32,"""gq""":96},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":33,"""dp""":33,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":20,"""dp""":20,"""gq""":60}} 3 0 0 0 0 TRUE 0 0 0 0 0.879165 1947 486 0 0 0 0 0 0.887927 12185 3122 0 51816 NM_017424.2 TRUE c.1082-1137T>C p.= {"coding_transcript_intron_variant"} 1137 ENSG00000093072 ENST00000262607.3 TRUE c.1082-1137T>C p.= {"coding_transcript_intron_variant"} 1137 +GRCh37 22 22 17664845 17664845 719 C CTT indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":4,"""gq""":12},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":5,"""dp""":12,"""gq""":61},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":2,"""dp""":2,"""gq""":6}} 1 1 1 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51816 NM_017424.2 TRUE c.1082-1195_1082-1194insAA p.= {"coding_transcript_intron_variant"} 1194 ENSG00000093072 ENST00000262607.3 TRUE c.1082-1195_1082-1194insAA p.= {"coding_transcript_intron_variant"} 1194 +GRCh37 22 22 17664845 17664845 719 C CTTT indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":4,"""dp""":4,"""gq""":12},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":7,"""dp""":12,"""gq""":61},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":2,"""gq""":6}} 1 1 1 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51816 NM_017424.2 TRUE c.1082-1195_1082-1194insAAA p.= {"coding_transcript_intron_variant"} 1194 ENSG00000093072 ENST00000262607.3 TRUE c.1082-1195_1082-1194insAAA p.= {"coding_transcript_intron_variant"} 1194 +GRCh37 22 22 17665080 17665080 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":40,"""dp""":40,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":38,"""dp""":38,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":45,"""dp""":45,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.877358 1938 495 0 0 0 0 0 0.885834 11962 3140 0 51816 NM_017424.2 TRUE c.1082-1429T>C p.= {"coding_transcript_intron_variant"} 1429 ENSG00000093072 ENST00000262607.3 TRUE c.1082-1429T>C p.= {"coding_transcript_intron_variant"} 1429 +GRCh37 22 22 17665144 17665144 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":42,"""dp""":42,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":34,"""dp""":34,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":53,"""dp""":53,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.877358 1938 495 0 0 0 0 0 0.886295 12226 3188 0 51816 NM_017424.2 TRUE c.1082-1493T>C p.= {"coding_transcript_intron_variant"} 1493 ENSG00000093072 ENST00000262607.3 TRUE c.1082-1493T>C p.= {"coding_transcript_intron_variant"} 1493 +GRCh37 22 22 17665413 17665413 719 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":32,"""dp""":32,"""gq""":96},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":32,"""dp""":32,"""gq""":96},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":47,"""dp""":47,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.877358 1938 495 0 0 0 0 0 0.885869 12280 3212 0 51816 NM_017424.2 TRUE c.1082-1762A>G p.= {"coding_transcript_intron_variant"} 1762 ENSG00000093072 ENST00000262607.3 TRUE c.1082-1762A>G p.= {"coding_transcript_intron_variant"} 1762 +GRCh37 22 22 17665661 17665661 719 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":18,"""dp""":18,"""gq""":54},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":19,"""dp""":19,"""gq""":57},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":27,"""dp""":27,"""gq""":81}} 3 0 0 0 0 FALSE 0 0 0 0 0.877358 1938 495 0 0 0 0 0 0.885306 11893 3122 0 51816 NM_017424.2 TRUE c.1082-2010T>G p.= {"coding_transcript_intron_variant"} 2010 ENSG00000093072 ENST00000262607.3 TRUE c.1082-2010T>G p.= {"coding_transcript_intron_variant"} 2010 +GRCh37 22 22 17665782 17665838 719 ACACTCTAGCCTGGGTGACAGAGGTGGAGGCTGTAGTGAGCTGTCATCACACCACCG A indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":16,"""dp""":16,"""gq""":49},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":18,"""dp""":18,"""gq""":57},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":17,"""dp""":17,"""gq""":55}} 3 0 0 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0.834212 7994 2373 0 51816 NM_017424.2 TRUE c.1082-2187_1082-2132del p.= {"coding_transcript_intron_variant"} 2131 ENSG00000093072 ENST00000262607.3 TRUE c.1082-2187_1082-2132del p.= {"coding_transcript_intron_variant"} 2131 +GRCh37 22 22 17665873 17665873 719 A AATATATATATATATATATATATATATATAT indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":3,"""dp""":3,"""gq""":13},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":6,"""dp""":17,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":0,"""dp""":17,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 51816 NM_017424.2 TRUE c.1082-2223_1082-2222insATATATATATATATATATATATATATATAT p.= {"coding_transcript_intron_variant"} 2222 ENSG00000093072 ENST00000262607.3 TRUE c.1082-2223_1082-2222insATATATATATATATATATATATATATATAT p.= {"coding_transcript_intron_variant"} 2222 +GRCh37 22 22 17666164 17666164 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":25,"""dp""":25,"""gq""":74},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":27,"""dp""":27,"""gq""":81},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":38,"""dp""":39,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.877358 1938 495 0 0 0 0 0 0.886538 11936 3116 0 51816 NM_017424.2 TRUE c.1082-2513G>A p.= {"coding_transcript_intron_variant"} 2513 ENSG00000093072 ENST00000262607.3 TRUE c.1082-2513G>A p.= {"coding_transcript_intron_variant"} 2513 +GRCh37 22 22 17666223 17666223 719 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":26,"""dp""":26,"""gq""":78},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":29,"""dp""":29,"""gq""":87},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":38,"""dp""":38,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.877358 1938 495 0 0 0 0 0 0.886468 12171 3158 0 51816 NM_017424.2 TRUE c.1082-2572C>T p.= {"coding_transcript_intron_variant"} 2572 ENSG00000093072 ENST00000262607.3 TRUE c.1082-2572C>T p.= {"coding_transcript_intron_variant"} 2572 +GRCh37 22 22 17666279 17666279 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":29,"""gq""":87},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":28,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":45,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.272381 286 785 0 0 0 0 0 0.222927 1004 4876 0 51816 NM_017424.2 TRUE c.1082-2628G>A p.= {"coding_transcript_intron_variant"} 2628 ENSG00000093072 ENST00000262607.3 TRUE c.1082-2628G>A p.= {"coding_transcript_intron_variant"} 2628 +GRCh37 22 22 17666280 17666280 719 T G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":29,"""dp""":29,"""gq""":87},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":27,"""dp""":27,"""gq""":81},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":45,"""dp""":45,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.876556 1935 497 0 0 0 0 0 0.88578 12161 3185 0 51816 NM_017424.2 TRUE c.1082-2629A>C p.= {"coding_transcript_intron_variant"} 2629 ENSG00000093072 ENST00000262607.3 TRUE c.1082-2629A>C p.= {"coding_transcript_intron_variant"} 2629 +GRCh37 22 22 17666306 17666316 719 AAAAATAAAAT A indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":22,"""dp""":22,"""gq""":67},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":24,"""dp""":24,"""gq""":73},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":30,"""dp""":30,"""gq""":91}} 3 0 0 0 0 FALSE 0 0 0 0 0.876957 1937 495 0 0 0 0 0 0.883708 11647 3090 0 51816 NM_017424.2 TRUE c.1082-2665_1082-2656del p.= {"coding_transcript_intron_variant"} 2655 ENSG00000093072 ENST00000262607.3 TRUE c.1082-2665_1082-2656del p.= {"coding_transcript_intron_variant"} 2655 +GRCh37 22 22 17666437 17666437 719 A T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":45,"""dp""":45,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":49,"""dp""":49,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":36,"""dp""":36,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.87776 1940 493 0 0 0 0 0 0.885891 12281 3216 0 51816 NM_017424.2 TRUE c.1082-2786T>A p.= {"coding_transcript_intron_variant"} 2786 ENSG00000093072 ENST00000262607.3 TRUE c.1082-2786T>A p.= {"coding_transcript_intron_variant"} 2786 +GRCh37 22 22 17666702 17666702 719 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":35,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":36,"""dp""":36,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":34,"""dp""":34,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.879366 1947 487 0 0 0 0 0 0.883223 12122 3279 0 51816 NM_017424.2 TRUE c.1081+2527A>G p.= {"coding_transcript_intron_variant"} 2527 ENSG00000093072 ENST00000262607.3 TRUE c.1081+2527A>G p.= {"coding_transcript_intron_variant"} 2527 +GRCh37 22 22 17666725 17666725 719 T G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":38,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":44,"""dp""":44,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":38,"""dp""":38,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.879566 1948 486 0 0 0 0 0 0.8836 12122 3266 0 51816 NM_017424.2 TRUE c.1081+2504A>C p.= {"coding_transcript_intron_variant"} 2504 ENSG00000093072 ENST00000262607.3 TRUE c.1081+2504A>C p.= {"coding_transcript_intron_variant"} 2504 +GRCh37 22 22 17666727 17666727 719 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":38,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":43,"""dp""":43,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":39,"""dp""":39,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.878964 1945 489 0 0 0 0 0 0.883585 12119 3268 0 51816 NM_017424.2 TRUE c.1081+2502A>G p.= {"coding_transcript_intron_variant"} 2502 ENSG00000093072 ENST00000262607.3 TRUE c.1081+2502A>G p.= {"coding_transcript_intron_variant"} 2502 +GRCh37 22 22 17667279 17667280 719 TG T indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":36,"""dp""":36,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":41,"""dp""":41,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":48,"""dp""":48,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 1.0 2491 0 0 0 0 0 0 1.0 15689 0 0 51816 NM_017424.2 TRUE c.1081+1949del p.= {"coding_transcript_intron_variant"} 1949 ENSG00000093072 ENST00000262607.3 TRUE c.1081+1949del p.= {"coding_transcript_intron_variant"} 1949 +GRCh37 22 22 17667426 17667426 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":38,"""dp""":39,"""gq""":91},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":46,"""dp""":46,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":36,"""dp""":36,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.624448 1027 1057 0 0 0 0 0 0.640303 6414 7047 0 51816 NM_017424.2 TRUE c.1081+1803G>A p.= {"coding_transcript_intron_variant"} 1803 ENSG00000093072 ENST00000262607.3 TRUE c.1081+1803G>A p.= {"coding_transcript_intron_variant"} 1803 +GRCh37 22 22 17667451 17667451 719 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":41,"""dp""":41,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":45,"""dp""":45,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":40,"""dp""":40,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.880369 1953 480 0 0 0 0 0 0.884468 12030 3217 0 51816 NM_017424.2 TRUE c.1081+1778C>T p.= {"coding_transcript_intron_variant"} 1778 ENSG00000093072 ENST00000262607.3 TRUE c.1081+1778C>T p.= {"coding_transcript_intron_variant"} 1778 +GRCh37 22 22 17667466 17667466 719 T A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":42,"""dp""":42,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":40,"""dp""":40,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":39,"""dp""":39,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.880169 1952 481 0 0 0 0 0 0.888268 12164 3171 0 51816 NM_017424.2 TRUE c.1081+1763A>T p.= {"coding_transcript_intron_variant"} 1763 ENSG00000093072 ENST00000262607.3 TRUE c.1081+1763A>T p.= {"coding_transcript_intron_variant"} 1763 +GRCh37 22 22 17667737 17667737 719 T TGACA indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":42,"""dp""":42,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":29,"""dp""":29,"""gq""":96},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":27,"""dp""":27,"""gq""":90}} 3 0 0 0 0 FALSE 0 0 0 0 0.877559 1940 492 0 0 0 0 0 0.885101 11864 3172 0 51816 NM_017424.2 TRUE c.1081+1491_1081+1492insTGTC p.= {"coding_transcript_intron_variant"} 1492 ENSG00000093072 ENST00000262607.3 TRUE c.1081+1491_1081+1492insTGTC p.= {"coding_transcript_intron_variant"} 1492 +GRCh37 22 22 17668056 17668056 719 C CA indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":26,"""dp""":27,"""gq""":58},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":25,"""dp""":26,"""gq""":56},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":27,"""dp""":27,"""gq""":80}} 3 0 0 0 0 FALSE 0 0 0 0 0.503011 526 1454 0 0 0 0 0 0.699943 4996 4851 0 51816 NM_017424.2 TRUE c.1081+1172_1081+1173insT p.= {"coding_transcript_intron_variant"} 1173 ENSG00000093072 ENST00000262607.3 TRUE c.1081+1172_1081+1173insT p.= {"coding_transcript_intron_variant"} 1173 +GRCh37 22 22 17668491 17668491 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":30,"""gq""":88},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":38,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":50,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.315737 313 947 0 0 0 0 0 0.264337 1192 5719 0 51816 NM_017424.2 TRUE c.1081+738G>A p.= {"coding_transcript_intron_variant"} 738 ENSG00000093072 ENST00000262607.3 TRUE c.1081+738G>A p.= {"coding_transcript_intron_variant"} 738 +GRCh37 22 22 17668568 17668568 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":36,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":20,"""dp""":39,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":24,"""dp""":50,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.267162 271 789 0 0 0 0 0 0.212419 902 4569 0 51816 NM_017424.2 TRUE c.1081+661T>C p.= {"coding_transcript_intron_variant"} 661 ENSG00000093072 ENST00000262607.3 TRUE c.1081+661T>C p.= {"coding_transcript_intron_variant"} 661 +GRCh37 22 22 17668765 17668765 719 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":37,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":27,"""gq""":81},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":31,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.195905 114 748 0 0 0 0 0 0.276868 1238 6077 0 51816 NM_017424.2 TRUE c.1081+464T>G p.= {"coding_transcript_intron_variant"} 464 ENSG00000093072 ENST00000262607.3 TRUE c.1081+464T>G p.= {"coding_transcript_intron_variant"} 464 +GRCh37 22 22 17668850 17668850 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":31,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":33,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":49,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.192894 116 729 0 0 0 0 0 0.272075 1157 6030 0 51816 NM_017424.2 TRUE c.1081+379G>A p.= {"coding_transcript_intron_variant"} 379 ENSG00000093072 ENST00000262607.3 TRUE c.1081+379G>A p.= {"coding_transcript_intron_variant"} 379 +GRCh37 22 22 17668851 17668851 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":32,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":33,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":49,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0.196708 118 744 0 0 0 0 0 0.275662 1171 6112 0 51816 NM_017424.2 TRUE c.1081+378T>C p.= {"coding_transcript_intron_variant"} 378 ENSG00000093072 ENST00000262607.3 TRUE c.1081+378T>C p.= {"coding_transcript_intron_variant"} 378 +GRCh37 22 22 17668983 17668983 719 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":23,"""dp""":43,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":36,"""dp""":36,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":12,"""dp""":31,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.571457 772 1303 0 0 0 0 0 0.552056 4490 6917 0 51816 NM_017424.2 TRUE c.1081+246C>T p.= {"coding_transcript_intron_variant"} 246 ENSG00000093072 ENST00000262607.3 TRUE c.1081+246C>T p.= {"coding_transcript_intron_variant"} 246 +GRCh37 22 22 17668992 17668994 719 GAA G indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":24,"""dp""":42,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":36,"""dp""":36,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":11,"""dp""":34,"""gq""":99}} 1 0 2 0 0 TRUE 0 0 0 0 0.60277 949 1105 0 0 0 0 0 0.555981 4605 6909 0 51816 NM_017424.2 TRUE c.1081+235_1081+236del p.= {"coding_transcript_intron_variant"} 235 ENSG00000093072 ENST00000262607.3 TRUE c.1081+235_1081+236del p.= {"coding_transcript_intron_variant"} 235 +GRCh37 22 22 17669151 17669151 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":47,"""dp""":47,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":34,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":47,"""gq""":99}} 1 1 1 0 0 TRUE 0 0 0 0 0.675231 1184 996 0 0 0 0 0 0.672399 7122 6829 0 51816 NM_017424.2 TRUE c.1081+78G>A p.= {"coding_transcript_intron_variant"} 78 ENSG00000093072 ENST00000262607.3 TRUE c.1081+78G>A p.= {"coding_transcript_intron_variant"} 78 +GRCh37 22 22 17669406 17669406 719 G C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":35,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":12,"""dp""":28,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":36,"""gq""":99}} 1 0 2 0 0 TRUE 0 0 0 0 0.562425 866 1070 0 0 0 0 0 0.683436 7504 6348 0 51816 NM_017424.2 TRUE c.973-69C>G p.= {"coding_transcript_intron_variant"} 69 ENSG00000093072 ENST00000262607.3 TRUE c.973-69C>G p.= {"coding_transcript_intron_variant"} 69 +GRCh37 22 22 17669469 17669469 719 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":43,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":29,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":36,"""gq""":99}} 0 1 2 0 0 TRUE 0 0 0 0 0.278202 228 930 0 0 0 0 0 0.344286 1908 6903 0 51816 NM_017424.2 TRUE c.973-132A>G p.= {"coding_transcript_intron_variant"} 132 ENSG00000093072 ENST00000262607.3 TRUE c.973-132A>G p.= {"coding_transcript_intron_variant"} 132 +GRCh37 22 22 17669686 17669686 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":15,"""dp""":15,"""gq""":45},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":14,"""dp""":14,"""gq""":42},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":18,"""dp""":18,"""gq""":54}} 3 0 0 0 0 FALSE 0 0 0 0 0.804295 1639 729 0 0 0 0 0 0.809164 8833 3984 0 51816 NM_017424.2 TRUE c.973-349T>C p.= {"coding_transcript_intron_variant"} 349 ENSG00000093072 ENST00000262607.3 TRUE c.973-349T>C p.= {"coding_transcript_intron_variant"} 349 +GRCh37 22 22 17669760 17669760 719 T A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":9,"""dp""":9,"""gq""":27},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":6,"""dp""":12,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":13,"""gq""":39}} 1 1 1 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0.299566 320 1155 0 51816 NM_017424.2 TRUE c.973-423A>T p.= {"coding_transcript_intron_variant"} 423 ENSG00000093072 ENST00000262607.3 TRUE c.973-423A>T p.= {"coding_transcript_intron_variant"} 423 +GRCh37 22 22 17669870 17669870 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":29,"""dp""":29,"""gq""":87},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":31,"""dp""":31,"""gq""":93},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":34,"""dp""":34,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.781614 1559 776 0 0 0 0 0 0.782287 8598 4453 0 51816 NM_017424.2 TRUE c.973-533T>C p.= {"coding_transcript_intron_variant"} 533 ENSG00000093072 ENST00000262607.3 TRUE c.973-533T>C p.= {"coding_transcript_intron_variant"} 533 +GRCh37 22 22 17669896 17669896 719 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":26,"""dp""":26,"""gq""":78},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":29,"""dp""":29,"""gq""":87},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":33,"""dp""":33,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.815134 1670 721 0 0 0 0 0 0.817912 9150 4047 0 51816 NM_017424.2 TRUE c.973-559T>G p.= {"coding_transcript_intron_variant"} 559 ENSG00000093072 ENST00000262607.3 TRUE c.973-559T>G p.= {"coding_transcript_intron_variant"} 559 +GRCh37 22 22 17669909 17669911 719 CTT C indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":15,"""dp""":15,"""gq""":45},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":20,"""dp""":20,"""gq""":60},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":17,"""dp""":18,"""gq""":33}} 3 0 0 0 0 FALSE 0 0 0 0 0.7222 1290 1018 0 0 0 0 0 0.473669 1512 3596 0 51816 NM_017424.2 TRUE c.973-574_973-573del p.= {"coding_transcript_intron_variant"} 572 ENSG00000093072 ENST00000262607.3 TRUE c.973-574_973-573del p.= {"coding_transcript_intron_variant"} 572 +GRCh37 22 22 17670256 17670256 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":46,"""dp""":46,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":37,"""dp""":37,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":37,"""dp""":37,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.613007 972 1110 0 0 0 0 0 0.574891 5196 7563 0 51816 NM_017424.2 TRUE c.972+576G>A p.= {"coding_transcript_intron_variant"} 576 ENSG00000093072 ENST00000262607.3 TRUE c.972+576G>A p.= {"coding_transcript_intron_variant"} 576 +GRCh37 22 22 17671133 17671133 719 C G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":51,"""dp""":51,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":48,"""dp""":48,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":49,"""dp""":49,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0.481333 618 1162 0 0 0 0 0 0.489595 3794 7752 0 51816 NM_017424.2 TRUE c.882-211G>C p.= {"coding_transcript_intron_variant"} 211 ENSG00000093072 ENST00000262607.3 TRUE c.882-211G>C p.= {"coding_transcript_intron_variant"} 211 +GRCh37 22 22 17673165 17673165 719 A C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":46,"""dp""":46,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":31,"""dp""":31,"""gq""":93},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":45,"""dp""":45,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 1.0 2491 0 0 0 0 0 0 1.0 15686 0 0 51816 NM_017424.2 TRUE c.754-465T>G p.= {"coding_transcript_intron_variant"} 465 ENSG00000093072 ENST00000262607.3 TRUE c.754-465T>G p.= {"coding_transcript_intron_variant"} 465 +GRCh37 22 22 17673719 17673720 719 GA G indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":34,"""dp""":34,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":37,"""dp""":37,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":28,"""dp""":28,"""gq""":84}} 3 0 0 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0.536169 3709 7391 0 51816 NM_017424.2 TRUE c.754-1020del p.= {"coding_transcript_intron_variant"} 1019 ENSG00000093072 ENST00000262607.3 TRUE c.754-1020del p.= {"coding_transcript_intron_variant"} 1019 +GRCh37 22 22 17674248 17674250 719 CAA C indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":5,"""gq""":4},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":4,"""dp""":7,"""gq""":37},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":6,"""dp""":10,"""gq""":48}} 0 1 2 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0.0539568 24 492 0 51816 NM_017424.2 TRUE c.754-1550_754-1549del p.= {"coding_transcript_intron_variant"} 1548 ENSG00000093072 ENST00000262607.3 TRUE c.754-1550_754-1549del p.= {"coding_transcript_intron_variant"} 1548 +GRCh37 22 22 17674248 17674249 719 CA C indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":4,"""dp""":5,"""gq""":4},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":3,"""dp""":7,"""gq""":37},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":4,"""dp""":10,"""gq""":48}} 0 0 3 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0.028777 11 266 0 51816 NM_017424.2 TRUE c.754-1550del p.= {"coding_transcript_intron_variant"} 1548 ENSG00000093072 ENST00000262607.3 TRUE c.754-1550del p.= {"coding_transcript_intron_variant"} 1548 +GRCh37 22 22 17674568 17674568 719 T TA indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":24,"""dp""":24,"""gq""":71},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":26,"""dp""":28,"""gq""":55},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":35,"""dp""":35,"""gq""":99}} 3 0 0 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0.569394 3193 6168 0 51816 NM_017424.2 TRUE c.754-1869_754-1868insT p.= {"coding_transcript_intron_variant"} 1868 ENSG00000093072 ENST00000262607.3 TRUE c.754-1869_754-1868insT p.= {"coding_transcript_intron_variant"} 1868 +GRCh37 22 22 17674909 17674909 719 G GA indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":20,"""gq""":60},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":9,"""dp""":19,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":10,"""dp""":24,"""gq""":99}} 0 1 2 0 0 FALSE 0 0 0 0 0 0 0 0 0 0 0 0 0.530227 2379 5416 0 51816 NM_017424.2 TRUE c.754-2210_754-2209insT p.= {"coding_transcript_intron_variant"} 2209 ENSG00000093072 ENST00000262607.3 TRUE c.754-2210_754-2209insT p.= {"coding_transcript_intron_variant"} 2209 +GRCh37 22 22 17675900 17675900 719 C A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":11,"""dp""":28,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":53,"""dp""":53,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.541148 794 1108 0 0 0 0 0 0.448263 3311 7388 0 51816 NM_017424.2 TRUE c.754-3200G>T p.= {"coding_transcript_intron_variant"} 3200 ENSG00000093072 ENST00000262607.3 TRUE c.754-3200G>T p.= {"coding_transcript_intron_variant"} 3200 +GRCh37 22 22 17676102 17676102 719 T A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":30,"""dp""":54,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":19,"""dp""":38,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":39,"""dp""":39,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.557407 833 1111 0 0 0 0 0 0.490608 3901 7555 0 51816 NM_017424.2 TRUE c.754-3402A>T p.= {"coding_transcript_intron_variant"} 3402 ENSG00000093072 ENST00000262607.3 TRUE c.754-3402A>T p.= {"coding_transcript_intron_variant"} 3402 +GRCh37 22 22 17676410 17676410 719 C A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":43,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":39,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":35,"""dp""":35,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.637696 1069 1039 0 0 0 0 0 0.521741 4181 7189 0 51816 NM_017424.2 TRUE c.754-3710G>T p.= {"coding_transcript_intron_variant"} 3710 ENSG00000093072 ENST00000262607.3 TRUE c.754-3710G>T p.= {"coding_transcript_intron_variant"} 3710 +GRCh37 22 22 17676414 17676414 719 G A snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":40,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":38,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":33,"""dp""":33,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.637495 1068 1040 0 0 0 0 0 0.522792 4173 7160 0 51816 NM_017424.2 TRUE c.754-3714C>T p.= {"coding_transcript_intron_variant"} 3714 ENSG00000093072 ENST00000262607.3 TRUE c.754-3714C>T p.= {"coding_transcript_intron_variant"} 3714 +GRCh37 22 22 17676418 17676418 719 C CA indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":35,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":37,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":33,"""dp""":33,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.523485 581 1446 0 0 0 0 0 0.522123 3994 7140 0 51816 NM_017424.2 TRUE c.754-3719_754-3718insT p.= {"coding_transcript_intron_variant"} 3718 ENSG00000093072 ENST00000262607.3 TRUE c.754-3719_754-3718insT p.= {"coding_transcript_intron_variant"} 3718 +GRCh37 22 22 17676590 17676590 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":26,"""dp""":49,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":16,"""dp""":32,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":53,"""dp""":53,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.134083 59 550 0 0 0 0 0 0.139134 349 3589 0 51816 NM_017424.2 TRUE c.754-3890T>C p.= {"coding_transcript_intron_variant"} 3890 ENSG00000093072 ENST00000262607.3 TRUE c.754-3890T>C p.= {"coding_transcript_intron_variant"} 3890 +GRCh37 22 22 17676604 17676604 719 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":45,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":30,"""gq""":93},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":21,"""dp""":50,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 0.00200723 0 10 0 0 0 0 0 0.00453427 2 136 0 51816 NM_017424.2 TRUE c.754-3904A>G p.= {"coding_transcript_intron_variant"} 3904 ENSG00000093072 ENST00000262607.3 TRUE c.754-3904A>G p.= {"coding_transcript_intron_variant"} 3904 +GRCh37 22 22 17676785 17676785 719 A G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":33,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":17,"""dp""":32,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":33,"""dp""":33,"""gq""":98}} 1 0 2 0 0 FALSE 0 0 0 0 0.721999 1349 899 0 0 0 0 0 0.591954 5687 6960 0 51816 NM_017424.2 TRUE c.754-4085T>C p.= {"coding_transcript_intron_variant"} 4085 ENSG00000093072 ENST00000262607.3 TRUE c.754-4085T>C p.= {"coding_transcript_intron_variant"} 4085 +GRCh37 22 22 17677175 17677175 719 T C snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":29,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":7,"""dp""":21,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":30,"""dp""":30,"""gq""":90}} 1 0 2 0 0 FALSE 0 0 0 0 0.274789 193 983 0 0 0 0 0 0.235866 872 5223 0 51816 NM_017424.2 TRUE c.754-4475A>G p.= {"coding_transcript_intron_variant"} 4475 ENSG00000093072 ENST00000262607.3 TRUE c.754-4475A>G p.= {"coding_transcript_intron_variant"} 4475 +GRCh37 22 22 17677213 17677213 719 C CA indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":26,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":7,"""dp""":15,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":22,"""dp""":22,"""gq""":66}} 1 0 2 0 0 FALSE 0 0 0 0 0.182658 89 732 0 0 0 0 0 0.387504 757 3336 0 51816 NM_017424.2 TRUE c.754-4514_754-4513insT p.= {"coding_transcript_intron_variant"} 4513 ENSG00000093072 ENST00000262607.3 TRUE c.754-4514_754-4513insT p.= {"coding_transcript_intron_variant"} 4513 +GRCh37 22 22 17677321 17677321 719 T G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":25,"""dp""":47,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":31,"""gq""":93},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""0/0""","""ad""":0,"""dp""":45,"""gq""":99}} 0 2 1 0 0 FALSE 0 0 0 0 2.00723E-4 0 1 0 0 0 0 0 0 0 0 0 51816 NM_017424.2 TRUE c.754-4621A>C p.= {"coding_transcript_intron_variant"} 4621 ENSG00000093072 ENST00000262607.3 TRUE c.754-4621A>C p.= {"coding_transcript_intron_variant"} 4621 +GRCh37 22 22 17677699 17677699 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":30,"""dp""":48,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":22,"""dp""":37,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":45,"""dp""":45,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.70273 1269 963 0 0 0 0 0 0.585983 5605 7143 0 51816 NM_017424.2 TRUE c.754-4999G>A p.= {"coding_transcript_intron_variant"} 4999 ENSG00000093072 ENST00000262607.3 TRUE c.754-4999G>A p.= {"coding_transcript_intron_variant"} 4999 +GRCh37 22 22 17678128 17678128 719 C G snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":18,"""dp""":40,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":35,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":36,"""dp""":36,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.714572 1308 944 0 0 0 0 0 0.596935 5779 6947 0 51816 NM_017424.2 TRUE c.754-5428G>C p.= {"coding_transcript_intron_variant"} 5428 ENSG00000093072 ENST00000262607.3 TRUE c.754-5428G>C p.= {"coding_transcript_intron_variant"} 5428 +GRCh37 22 22 17678159 17678159 719 C CT indel . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":13,"""dp""":29,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":11,"""dp""":31,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":37,"""dp""":37,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.170413 58 733 0 0 0 0 0 0.188241 432 3868 0 51816 NM_017424.2 TRUE c.754-5460_754-5459insA p.= {"coding_transcript_intron_variant"} 5459 ENSG00000093072 ENST00000262607.3 TRUE c.754-5460_754-5459insA p.= {"coding_transcript_intron_variant"} 5459 +GRCh37 22 22 17678195 17678195 719 C T snv . . {} {"""Case_1_father-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":14,"""dp""":38,"""gq""":99},"""Case_1_index-N1-DNA1-WGS1""":{"""gt""":"""0/1""","""ad""":15,"""dp""":43,"""gq""":99},"""Case_1_mother-N1-DNA1-WGS1""":{"""gt""":"""1/1""","""ad""":45,"""dp""":45,"""gq""":99}} 1 0 2 0 0 FALSE 0 0 0 0 0.253713 180 904 0 0 0 0 0 0.235237 879 5269 0 51816 NM_017424.2 TRUE c.754-5495G>A p.= {"coding_transcript_intron_variant"} 5495 ENSG00000093072 ENST00000262607.3 TRUE c.754-5495G>A p.= {"coding_transcript_intron_variant"} 5495 diff --git a/tests/hg19-chr22/Case_1_index.gatk_hc.vcf.gz b/tests/hg19-chr22/Case_1_index.gatk_hc.vcf.gz new file mode 100644 index 0000000..b11a90e --- /dev/null +++ b/tests/hg19-chr22/Case_1_index.gatk_hc.vcf.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:bff1093c392e0171d17190464ea3f89d353539f261565b70543a32d2ecc96f6d +size 19137 diff --git a/tests/hg19-chr22/Case_1_index.gatk_hc.vcf.gz.tbi b/tests/hg19-chr22/Case_1_index.gatk_hc.vcf.gz.tbi new file mode 100644 index 0000000..e557f18 --- /dev/null +++ b/tests/hg19-chr22/Case_1_index.gatk_hc.vcf.gz.tbi @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:5e2759138dbf58f491baf9e0c13f5ec5a0b4159bf60c83824420ffe8e85d5b9b +size 209 diff --git a/tests/hg19-chr22/Clinvar.tsv b/tests/hg19-chr22/Clinvar.tsv new file mode 100644 index 0000000..35ee730 --- /dev/null +++ b/tests/hg19-chr22/Clinvar.tsv @@ -0,0 +1 @@ +release chromosome start end bin reference alternative clinvar_version set_type variation_type symbols hgnc_ids vcv summary_clinvar_review_status_label summary_clinvar_pathogenicity_label summary_clinvar_pathogenicity summary_clinvar_gold_stars 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a/tests/hg19-chr22/ExAC.r1.sites.vep.vcf.gz.tbi b/tests/hg19-chr22/ExAC.r1.sites.vep.vcf.gz.tbi new file mode 100644 index 0000000..8eb0e92 --- /dev/null +++ b/tests/hg19-chr22/ExAC.r1.sites.vep.vcf.gz.tbi @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:631a5d530fb083148b07b85e53137f2414f7d5c484a57a77df426447ee5768cf +size 231 diff --git a/tests/hg19-chr22/HgmdPublicLocus.tsv.gz b/tests/hg19-chr22/HgmdPublicLocus.tsv.gz new file mode 100644 index 0000000000000000000000000000000000000000..b7f1a39e7fd8b99f956d28a98f1955559a017b6d GIT binary patch literal 187 zcmV;s07U;EiwFo<7$0K*14w6WWKeZtY-wXmZ)0_HE_8EtE_7{h0Cmqn3j!e!hT-${ zYt}Jm^t^|?NB6K2R!9Y1`u)YyY|z^60bf4G8Xm#70Jpi8R9Z;^+T!a1A>ZK|Gdz8b zeu*VtvQObKoyJ)+AcA5dWTyp3VCCSvFRZ|=#rRuTMFQ>?+K>|9T1>mb8Ugh;=nLK5 paHy34dw=1chr22.fa.tmp + mv chr22.fa.tmp chr22.fa +fi + +if [[ ! -e chr22_part.fa.fai ]]; then + samtools faidx chr22.fa chr22:1-22,000,000 > chr22_part.fa.tmp + perl -p -i -e 's/^>chr.*/>22/g' chr22_part.fa.tmp + gzip -c chr22_part.fa.tmp >chr22_part.fa.gz + mv chr22_part.fa.tmp chr22_part.fa + samtools faidx chr22_part.fa +fi + +# ADA2(hg19): 22:17,660,192-17,680,545 +# GAB4(hg19): 22:17,442,827-17,489,112 + +if [[ ! -e hg19_refseq.ser ]]; then + jannovar -Xmx4096m download -d hg19/ensembl --gene-ids ENSG00000093072 ENSG00000215568 # ADA2 GAB4 + cp data/hg19_refseq.ser hg19_refseq.ser.tmp + mv hg19_refseq.ser.tmp hg19_refseq.ser +fi + +if [[ ! -e hg19_ensembl.ser ]]; then + jannovar -Xmx4096m download -d hg19/ensembl --gene-ids 51816 128954 # ADA2 GAB4 + cp data/hg19_ensembl.ser hg19_ensembl.ser.tmp + mv hg19_ensembl.ser.tmp hg19_ensembl.ser +fi + +REGIONS="22:17,660,192-17,680,545 22:17,442,827-17,489,112" +BASEDIR=/fast/groups/cubi/work/projects/2021-07-20_varfish-db-downloader-holtgrewe/varfish-db-downloader + +( \ + tabix --only-header $BASEDIR/GRCh37/ExAC/r1/download/ExAC.r1.sites.vep.vcf.gz $REGIONS; \ + tabix $BASEDIR/GRCh37/ExAC/r1/download/ExAC.r1.sites.vep.vcf.gz $REGIONS \ + | sort -k1,1V -k2,2n \ + | uniq; \ +) \ +| bgzip -c \ +> ExAC.r1.sites.vep.vcf.gz +tabix -f ExAC.r1.sites.vep.vcf.gz + +( \ + tabix --only-header $BASEDIR/GRCh37/gnomAD_exomes/r2.1.1/download/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz $REGIONS; \ + tabix $BASEDIR/GRCh37/gnomAD_exomes/r2.1.1/download/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz $REGIONS \ + | sort -k1,1V -k2,2n \ + | uniq; \ +) \ +| bgzip -c \ +> gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz +tabix -f gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz + +( \ + tabix --only-header $BASEDIR/GRCh37/gnomAD_genomes/r2.1.1/download/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz $REGIONS; \ + tabix $BASEDIR/GRCh37/gnomAD_genomes/r2.1.1/download/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz $REGIONS \ + | sort -k1,1V -k2,2n \ + | uniq; \ +) \ +| bgzip -c \ +> gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz +tabix -f gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz + +( \ + tabix --only-header $BASEDIR/GRCh37/thousand_genomes/phase3/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz; \ + tabix $BASEDIR/GRCh37/thousand_genomes/phase3/ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz $REGIONS \ + | sort -k1,1V -k2,2n \ + | uniq; \ +) \ +| bgzip -c \ +> ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz +tabix -f ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz + +(head -n 1 /tmp/Clinvar.tsv; tail -n +2 /tmp/Clinvar.tsv | sort -k2,2V -k3,3n -k4,4n) \ +| bgzip -c >/tmp/Clinvar.tsv.gz +tabix -S 1 -b 3 -e 4 -s 2 -f /tmp/Clinvar.tsv.gz +head -n 1 /tmp/Clinvar.tsv >Clinvar.tsv.tmp +tabix /tmp/Clinvar.tsv.gz $REGIONS \ +>>Clinvar.tsv.tmp +gzip Clinvar.tsv.tmp +mv Clinvar.tsv.tmp.gz Clinvar.tsv.gz + +(head -n 1 /tmp/HgmdPublicLocus.tsv; tail -n +2 /tmp/HgmdPublicLocus.tsv | sort -k2,2V -k3,3n -k4,4n) \ +| bgzip -c >/tmp/HgmdPublicLocus.tsv.gz +tabix -S 1 -b 3 -e 4 -s 2 -f /tmp/HgmdPublicLocus.tsv.gz +head -n 1 /tmp/HgmdPublicLocus.tsv >HgmdPublicLocus.tsv.tmp +tabix /tmp/HgmdPublicLocus.tsv.gz $REGIONS \ +>>HgmdPublicLocus.tsv.tmp +gzip HgmdPublicLocus.tsv.tmp +mv HgmdPublicLocus.tsv.tmp.gz HgmdPublicLocus.tsv.gz + +BASEDIR=/fast/groups/cubi/work/projects/2022-07-06_VarFish_Course_Data/snappy-processing/ +VCF=$BASEDIR/variant_calling/output/bwa.gatk_hc.Case_1_index-N1-DNA1-WGS1/out/bwa.gatk_hc.Case_1_index-N1-DNA1-WGS1.vcf.gz + +( \ + tabix --only-header $VCF $REGIONS; \ + tabix $VCF $REGIONS \ + | sort -k1,1V -k2,2n \ + | uniq; \ +) \ +| bgzip -c \ +> Case_1_index.gatk_hc.vcf.gz +tabix -f Case_1_index.gatk_hc.vcf.gz + +VCF=$BASEDIR/wgs_sv_calling/output/bwa.delly2.Case_1_index-N1-DNA1-WGS1/out/bwa.delly2.Case_1_index-N1-DNA1-WGS1.vcf.gz + +( \ + tabix --only-header $VCF $REGIONS; \ + tabix $VCF $REGIONS \ + | sort -k1,1V -k2,2n \ + | uniq; \ +) \ +| bgzip -c \ +> Case_1_index.delly2.vcf.gz +tabix -f Case_1_index.delly2.vcf.gz diff --git a/tests/hg19-chr22/chr22_part.fa.fai b/tests/hg19-chr22/chr22_part.fa.fai new file mode 100644 index 0000000..a74c363 --- /dev/null +++ b/tests/hg19-chr22/chr22_part.fa.fai @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a86867ee70318ae675b4828339dad749a9e11127209608c73dda9777b48966e8 +size 20 diff --git a/tests/hg19-chr22/chr22_part.fa.gz b/tests/hg19-chr22/chr22_part.fa.gz new file mode 100644 index 0000000..9c79b7e --- /dev/null +++ b/tests/hg19-chr22/chr22_part.fa.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f433af004f3b5ea34e4b461da133d6ff67e080916c647854632055f2a097def1 +size 1845078 diff --git a/tests/hg19-chr22/db-info.txt-expected b/tests/hg19-chr22/db-info.txt-expected new file mode 100644 index 0000000..199d786 --- /dev/null +++ b/tests/hg19-chr22/db-info.txt-expected @@ -0,0 +1,12 @@ +Table clinvar_var +TABLE RELEASE CHROM COUNT +clinvar_var GRCh37 22 124 +Table hgmd_locus +TABLE RELEASE CHROM COUNT +hgmd_locus GRCh37 22 11 +Table gnomad_exome_var +TABLE RELEASE CHROM COUNT +gnomad_exome_var GRCh37 22 1437 +Table gnomad_genome_var +TABLE RELEASE CHROM COUNT +gnomad_genome_var GRCh37 22 6072 diff --git a/tests/hg19-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz b/tests/hg19-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz new file mode 100644 index 0000000..6e97ed1 --- /dev/null +++ b/tests/hg19-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:a0e957eaac9e9563ecaed7ee66ab413cf94b5ce779c25d1bdba149a08b76b7af +size 4599804 diff --git a/tests/hg19-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz.tbi b/tests/hg19-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz.tbi new file mode 100644 index 0000000..64b8d03 --- /dev/null +++ b/tests/hg19-chr22/gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz.tbi @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9a5e793df728aa6cc303e6d7ae60989a65f9e50a658d6df5c498cf55e85c47c6 +size 232 diff --git a/tests/hg19-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz b/tests/hg19-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz new file mode 100644 index 0000000..9a39c60 --- /dev/null +++ b/tests/hg19-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:04008d7b9f0ad93eb1fbbf93c9eeb2c44be0182a4167c2aeca96591e89dc643b +size 11012735 diff --git a/tests/hg19-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz.tbi b/tests/hg19-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz.tbi new file mode 100644 index 0000000..017c518 --- /dev/null +++ b/tests/hg19-chr22/gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz.tbi @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:927d47d06fea7aa320539a8ce70406704d340f504d7c8784d53741588ccdf652 +size 252 diff --git a/tests/hg19-chr22/hg19_ensembl.ser b/tests/hg19-chr22/hg19_ensembl.ser new file mode 100644 index 0000000..7cc5a5e --- /dev/null +++ b/tests/hg19-chr22/hg19_ensembl.ser @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ab93ed7b30af2aad73a786355317980e8b37fd0c84a71d78ee2918755ab3e847 +size 6801 diff --git a/tests/hg19-chr22/hg19_refseq.ser b/tests/hg19-chr22/hg19_refseq.ser new file mode 100644 index 0000000..201ff7c --- /dev/null +++ b/tests/hg19-chr22/hg19_refseq.ser @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:fb3233d5fc1ca0b9b67f43387062f63b7773473f4c2ede3721813c95018f2539 +size 5698 diff --git a/tests/hg19-chr22/run-tests.sh b/tests/hg19-chr22/run-tests.sh new file mode 100755 index 0000000..16131d4 --- /dev/null +++ b/tests/hg19-chr22/run-tests.sh @@ -0,0 +1,94 @@ +#!/usr/bin/bash + +set -euo pipefail +set -x + +JAR=$(ls ../../varfish-annotator-cli/target/varfish-annotator-cli-*.jar | grep -v sources | tail -n 1) + +## prepare + +gzip -d -k chr22_part.fa.gz + +## step 0: help + +java -jar $JAR --help >/tmp/the-output +test -s /tmp/the-output + +set +e +java -jar $JAR > /tmp/the-output +retcode=$? +set -e +test 1 -eq $retcode +test -s /tmp/the-output + +## step 1: init-db + +java -jar $JAR init-db \ + --release GRCh37 \ + --db-release-info varfish-annotator:main \ + --db-release-info varfish-annotator-db:for-testing \ + --db-path /tmp/out \ + \ + --ref-path chr22_part.fa \ + \ + --db-release-info exac:r1.0 \ + --exac-path ExAC.r1.sites.vep.vcf.gz \ + \ + --db-release-info thousand_genomes:v3.20101123 \ + --thousand-genomes-path ALL.chr22.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.vcf.gz \ + \ + --db-release-info clinvar:for-testing \ + --clinvar-path Clinvar.tsv.gz \ + \ + --db-release-info gnomad_exomes:r2.1.1 \ + --gnomad-exomes-path gnomad.exomes.r2.1.1.sites.chr22.vcf.bgz \ + \ + --db-release-info gnomad_genomes:r2.1.1 \ + --gnomad-genomes-path gnomad.genomes.r2.1.1.sites.chr22.vcf.bgz \ + \ + --db-release-info hgmd_public:for-testing \ + --hgmd-public HgmdPublicLocus.tsv.gz + +## step 2: db-info + +java -jar $JAR db-stats --db-path /tmp/out.h2.db --parseable \ +> /tmp/db-info.txt +diff /tmp/db-info.txt db-info.txt-expected + +## step 3: annotate + +java -jar $JAR annotate \ + --release GRCh37 \ + --input-vcf Case_1_index.gatk_hc.vcf.gz \ + --output-gts /tmp/Case_1_index.gatk_hc.gts.tsv \ + --output-db-info /tmp/Case_1_index.gatk_hc.db-info.tsv \ + --ref-path chr22_part.fa \ + --refseq-ser-path hg19_refseq.ser \ + --ensembl-ser-path hg19_ensembl.ser \ + --db-path /tmp/out.h2.db \ + --self-test-chr22-only + +diff /tmp/Case_1_index.gatk_hc.gts.tsv Case_1_index.gatk_hc.gts.tsv-expected +diff /tmp/Case_1_index.gatk_hc.db-info.tsv Case_1_index.gatk_hc.db-info.tsv-expected + +## step 4: annotate-svs + +java -jar $JAR annotate-svs \ + --release GRCh37 \ + --input-vcf Case_1_index.delly2.vcf.gz \ + --output-gts /tmp/Case_1_index.delly2.gts.tsv \ + --output-feature-effects /tmp/Case_1_index.delly2.feature-effects.tsv \ + --output-db-info /tmp/Case_1_index.delly2.db-info.tsv \ + --refseq-ser-path hg19_refseq.ser \ + --ensembl-ser-path hg19_ensembl.ser \ + --db-path /tmp/out.h2.db \ + --self-test-chr22-only + +diff /tmp/Case_1_index.delly2.gts.tsv Case_1_index.delly2.gts.tsv-expected +diff /tmp/Case_1_index.delly2.db-info.tsv Case_1_index.delly2.db-info.tsv-expected +diff /tmp/Case_1_index.delly2.feature-effects.tsv Case_1_index.delly2.feature-effects.tsv-expected + +## if we reach here, everything is fine + +echo "-- ALL TESTS PASSED --" +exit 0 diff --git a/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/VarfishAnnotatorCli.java b/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/VarfishAnnotatorCli.java index a64d75e..431e298 100644 --- a/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/VarfishAnnotatorCli.java +++ b/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/VarfishAnnotatorCli.java @@ -30,6 +30,9 @@ public static void main(String[] args) { if ((args == null || args.length == 0)) { jc.usage(); System.exit(1); + } else if (args.length == 1 && "--help".equals(args[0])) { + jc.usage(); + System.exit(0); } try { diff --git a/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate/AnnotateArgs.java b/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate/AnnotateArgs.java index 0eeb255..16ee1b7 100644 --- a/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate/AnnotateArgs.java +++ b/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate/AnnotateArgs.java @@ -47,6 +47,12 @@ public final class AnnotateArgs { hidden = true) private boolean selfTestChr1Only = false; + @Parameter( + names = "--self-test-chr22-only", + description = "Self-test with chr22 only (for tests)", + hidden = true) + private boolean selfTestChr22Only = false; + @Parameter(names = "--case-id", description = "The value to use for case ID") private String caseId = "."; @@ -110,6 +116,10 @@ public boolean isSelfTestChr1Only() { return selfTestChr1Only; } + public boolean isSelfTestChr22Only() { + return selfTestChr22Only; + } + public String getCaseId() { return caseId; } @@ -160,6 +170,8 @@ public String toString() { + '\'' + ", selfTestChr1Only=" + selfTestChr1Only + + ", selfTestChr22Only=" + + selfTestChr22Only + ", caseId='" + caseId + '\'' diff --git a/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate/AnnotateVcf.java b/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate/AnnotateVcf.java index a1cf721..c7945b5 100644 --- a/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate/AnnotateVcf.java +++ b/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate/AnnotateVcf.java @@ -170,7 +170,8 @@ public void run() { GzipUtil.maybeOpenGzipOutputStream(dbInfoStream, args.getOutputDbInfos()); BufferedWriter dbInfoBufWriter = new BufferedWriter(dbInfoWriter); ) { new VcfCompatibilityChecker(reader).check(args.getRelease()); - new DatabaseSelfTest(conn).selfTest(args.getRelease(), args.isSelfTestChr1Only()); + new DatabaseSelfTest(conn) + .selfTest(args.getRelease(), args.isSelfTestChr1Only(), args.isSelfTestChr22Only()); System.err.println("Deserializing Jannovar file..."); JannovarData refseqJvData = new JannovarDataSerializer(args.getRefseqSerPath()).load(); diff --git a/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateSvsArgs.java b/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateSvsArgs.java index b562193..845a051 100644 --- a/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateSvsArgs.java +++ b/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateSvsArgs.java @@ -41,6 +41,12 @@ public final class AnnotateSvsArgs { hidden = true) private boolean selfTestChr1Only = false; + @Parameter( + names = "--self-test-chr22-only", + description = "Self-test with chr22 only (for tests)", + hidden = true) + private boolean selfTestChr22Only = false; + @Parameter(names = "--case-id", description = "The value to use for case ID") private String caseId = "."; @@ -122,6 +128,10 @@ public boolean isSelfTestChr1Only() { return selfTestChr1Only; } + public boolean isSelfTestChr22Only() { + return selfTestChr22Only; + } + public String getCaseId() { return caseId; } @@ -205,6 +215,8 @@ public String toString() { + '\'' + ", selfTestChr1Only=" + selfTestChr1Only + + ", selfTestChr22Only=" + + selfTestChr22Only + ", caseId='" + caseId + '\'' diff --git a/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateSvsVcf.java b/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateSvsVcf.java index 2046eaf..2d86f56 100644 --- a/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateSvsVcf.java +++ b/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/annotate_svs/AnnotateSvsVcf.java @@ -185,7 +185,8 @@ public void run() { GenomeVersion genomeVersion = new VcfCompatibilityChecker(reader).guessGenomeVersion(); new VcfCompatibilityChecker(reader).check(args.getRelease()); - new DatabaseSelfTest(conn).selfTest(args.getRelease(), args.isSelfTestChr1Only()); + new DatabaseSelfTest(conn) + .selfTest(args.getRelease(), args.isSelfTestChr1Only(), args.isSelfTestChr22Only()); System.err.println("Deserializing Jannovar file..."); JannovarData refseqJvData = new JannovarDataSerializer(args.getRefseqSerPath()).load(); diff --git a/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/utils/DatabaseSelfTest.java b/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/utils/DatabaseSelfTest.java index 6dd25be..799d650 100644 --- a/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/utils/DatabaseSelfTest.java +++ b/varfish-annotator-cli/src/main/java/com/github/bihealth/varfish_annotator/utils/DatabaseSelfTest.java @@ -23,10 +23,13 @@ public DatabaseSelfTest(Connection conn) { this.conn = conn; } - public void selfTest(String release, boolean checkChr1Only) throws SelfTestFailedException { + public void selfTest(String release, boolean checkChr1Only, boolean checkChr22Only) + throws SelfTestFailedException { final List chromNames; if (checkChr1Only) { chromNames = CHROMS.subList(0, 1); + } else if (checkChr22Only) { + chromNames = CHROMS.subList(21, 22); } else { chromNames = CHROMS; }