diff --git a/.gitattributes b/.gitattributes index a18efe27..aed97b2a 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,2 +1,4 @@ tests/db/compile/** filter=lfs diff=lfs merge=lfs -text tests/db/hpo/** filter=lfs diff=lfs merge=lfs -text +tests/seqvars/ingest/db/grch37/** filter=lfs diff=lfs merge=lfs -text +tests/seqvars/ingest/db/grch38/** filter=lfs diff=lfs merge=lfs -text diff --git a/Cargo.lock b/Cargo.lock index ce5a457f..9a5384b2 100644 --- a/Cargo.lock +++ b/Cargo.lock @@ -1456,6 +1456,12 @@ version = "2.1.0" source = "registry+https://github.com/rust-lang/crates.io-index" checksum = "9a3a5bfb195931eeb336b2a7b4d761daec841b97f947d34394601737a7bba5e4" +[[package]] +name = "hxdmp" +version = "0.2.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a17b27f28a7466846baca75f0a5244e546e44178eb7f1c07a3820f413e91c6b0" + [[package]] name = "iana-time-zone" version = "0.1.57" @@ -1789,9 +1795,9 @@ dependencies = [ [[package]] name = "mehari" -version = "0.8.0" +version = "0.10.0" source = "registry+https://github.com/rust-lang/crates.io-index" -checksum = "876048178b1469372ec642af0d6c616aeac0f7dc18c405518a5779d41077ea5d" +checksum = "a95119609578b3515e0b3720c1a21a7a38cd2303a7557f5c0771372fc3d1fe4c" dependencies = [ "actix-web", "annonars", @@ -3436,17 +3442,21 @@ dependencies = [ "flate2", "float-cmp", "hgvs", + "hxdmp", "indexmap 2.0.2", "insta", "itertools", "log", "mehari", "multimap 0.9.0", + "noodles-bgzf", + "noodles-vcf", "pretty_assertions", "procfs", "prost", "prost-build", "regex", + "rocksdb", "rstest", "serde", "serde-jsonlines", diff --git a/Cargo.toml b/Cargo.toml index 376aaddc..7572b6a6 100644 --- a/Cargo.toml +++ b/Cargo.toml @@ -29,7 +29,7 @@ hgvs = "0.11" indexmap = { version = "2.0", features = ["serde"] } itertools = "0.11" log = "0.4" -mehari = "0.8" +mehari = "0.10" multimap = "0.9" procfs = "0.15" prost = "0.12" @@ -47,6 +47,9 @@ thousands = "0.2" tracing = "0.1" tracing-subscriber = "0.3" uuid = { version = "1.4", features = ["v4", "fast-rng", "serde"] } +noodles-vcf = "0.40.0" +rocksdb = { version = "0.21.0", features = ["multi-threaded-cf"] } +noodles-bgzf = "0.24.0" [build-dependencies] @@ -55,6 +58,7 @@ prost-build = "0.12" [dev-dependencies] file_diff = "1.0" float-cmp = "0.9.0" +hxdmp = "0.2.1" insta = { version = "1.32", features = ["yaml"] } pretty_assertions = "1.4" rstest = "0.18.2" diff --git a/README.md b/README.md index b0827246..992fa3dd 100644 --- a/README.md +++ b/README.md @@ -71,6 +71,62 @@ $ varfish-server-worker db mk-inhouse \ [--path-input-tsvs @IN/path-list2.txt] ``` +## The `seqvars ingest` Command + +This command takes as the input a single VCF file from a (supported) variant caller and converts it into a file for further querying. +The command interprets the following fields which are written out by the commonly used variant callers such as GATK UnifiedGenotyper, GATK HaplotypeCaller, and Illumina Dragen. + +- `FORMAT/GT` -- genotype +- `FORMAT/GQ` -- genotype quality +- `FORMAT/DP` -- total read coverage +- `FORMAT/AD` -- allelic depth, one value per allele (including reference0) +- `FORMAT/PS` -- physical phasing information as written out by GATK HaplotypeCaller in GVCF workflow and Dragen variant caller +- `FORMAT/SQ` -- "somatic quality" for each alternate allele, as written out by Illumina Dragen variant caller + - this field will be written as `FORMAT/GQ` + +The `seqvars ingest` command will annotate the variants with the following information: + +- gnomAD genomes and exomes allele frequencies +- gnomAD-mtDNA and HelixMtDb allele frequencies +- functional annotation following the [VCF ANN field standard](https://pcingola.github.io/SnpEff/adds/VCFannotationformat_v1.0.pdf) + +The command will emit one output line for each variant allele from the input and each affected gene. +That is, if two variant alleles affect two genes, four records will be written to the output file. +The annotation will be written out for one highest impact. + +Overall, the command will emit the following header rows in addition to the `##contig=` lines. + +``` +##fileformat=VCFv4.2 +##FILTER= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##x-varfish-version= +##x-varfish-version= +##x-varfish-version= +``` + +> [!NOTE] +> The gnomad-mtDNA information is written to the `INFO/gnomdad_genome_*` fields. + +> [!NOTE] +> Future versions of the worker will annotate the worst effect on a MANE select or MANE Clinical transcript. + # Developer Information This section is only relevant for developers of `varfish-server-worker`. diff --git a/src/common.rs b/src/common.rs index 33dea389..fee69574 100644 --- a/src/common.rs +++ b/src/common.rs @@ -23,6 +23,14 @@ pub struct Args { pub verbose: Verbosity, } +impl Default for Args { + fn default() -> Self { + Self { + verbose: Verbosity::new(0, 0), + } + } +} + /// Helper to print the current memory resident set size via `tracing`. pub fn trace_rss_now() { let me = procfs::process::Process::myself().unwrap(); diff --git a/src/main.rs b/src/main.rs index fc2103c6..6ea9bca6 100644 --- a/src/main.rs +++ b/src/main.rs @@ -2,6 +2,7 @@ pub mod common; pub mod db; +pub mod seqvars; pub mod sv; use clap::{Args, Parser, Subcommand}; @@ -33,6 +34,8 @@ enum Commands { Db(Db), /// SV filtration related commands. Sv(Sv), + /// Sequence variant related commands. + Seqvars(Seqvars), } /// Parsing of "db *" sub commands. @@ -67,6 +70,21 @@ enum SvCommands { Query(sv::query::Args), } +/// Parsing of "seqvars *" sub commands. +#[derive(Debug, Args)] +#[command(args_conflicts_with_subcommands = true)] +struct Seqvars { + /// The sub command to run + #[command(subcommand)] + command: SeqvarsCommands, +} + +/// Enum supporting the parsing of "sv *" sub commands. +#[derive(Debug, Subcommand)] +enum SeqvarsCommands { + Ingest(seqvars::ingest::Args), +} + fn main() -> Result<(), anyhow::Error> { let cli = Cli::parse(); @@ -98,6 +116,11 @@ fn main() -> Result<(), anyhow::Error> { db::to_bin::cli::run(&cli.common, args)?; } }, + Commands::Seqvars(seqvars) => match &seqvars.command { + SeqvarsCommands::Ingest(args) => { + seqvars::ingest::run(&cli.common, args)?; + } + }, Commands::Sv(sv) => match &sv.command { SvCommands::Query(args) => { sv::query::run(&cli.common, args)?; diff --git a/src/seqvars/ingest/header.rs b/src/seqvars/ingest/header.rs new file mode 100644 index 00000000..ac857839 --- /dev/null +++ b/src/seqvars/ingest/header.rs @@ -0,0 +1,514 @@ +use std::collections::HashSet; + +use noodles_vcf as vcf; + +use crate::common::GenomeRelease; + +/// Enumeration for the known variant callers. +#[derive(Debug, Clone, PartialEq, Eq, serde::Deserialize, serde::Serialize)] +pub enum VariantCaller { + GatkHaplotypeCaller { version: String }, + GatkUnifiedGenotyper { version: String }, + Dragen { version: String }, + Other, +} + +impl VariantCaller { + /// Return a string with the name of the variant caller for the VCF header string. + fn name(&self) -> &'static str { + match self { + VariantCaller::GatkHaplotypeCaller { .. } => "GatkHaplotypeCaller", + VariantCaller::GatkUnifiedGenotyper { .. } => "GatkUnifiedGenotyper", + VariantCaller::Dragen { .. } => "Dragen", + VariantCaller::Other => "Other", + } + } +} + +impl VariantCaller { + pub fn guess(header: &vcf::Header) -> Option { + for (other, collection) in header.other_records() { + if ["GATKCommandLine", "DRAGENCommandLine"] + .iter() + .any(|k| other.as_ref().starts_with(k)) + { + use vcf::header::record::value::collection::Collection; + if let Collection::Structured(map) = collection { + for (key, values) in map.iter() { + match (key.as_str(), values.other_fields().get("Version").cloned()) { + ("HaplotypeCaller", Some(version)) => { + return Some(VariantCaller::GatkHaplotypeCaller { version }) + } + ("UnifiedGenotyper", Some(version)) => { + return Some(VariantCaller::GatkUnifiedGenotyper { version }) + } + ("dragen", Some(version)) => { + return Some(VariantCaller::Dragen { version }) + } + _ => (), + } + } + } + } + } + None + } +} + +/// Add contigs for GRCh37. +fn add_contigs_37(builder: vcf::header::Builder) -> Result { + use vcf::header::record::value::map::Contig; + use vcf::header::record::value::Map; + + let mut builder = builder; + + let specs: &[(&str, usize); 25] = &[ + ("1", 249250621), + ("2", 243199373), + ("3", 198022430), + ("4", 191154276), + ("5", 180915260), + ("6", 171115067), + ("7", 159138663), + ("8", 146364022), + ("9", 141213431), + ("10", 135534747), + ("11", 135006516), + ("12", 133851895), + ("13", 115169878), + ("14", 107349540), + ("15", 102531392), + ("16", 90354753), + ("17", 81195210), + ("18", 78077248), + ("19", 59128983), + ("20", 63025520), + ("21", 48129895), + ("22", 51304566), + ("X", 155270560), + ("Y", 59373566), + ("MT", 16569), + ]; + + for (contig, length) in specs { + builder = builder.add_contig( + contig + .parse() + .map_err(|_| anyhow::anyhow!("invalid contig: {}", contig))?, + Map::::builder() + .set_length(*length) + .insert( + "assembly" + .parse() + .map_err(|_| anyhow::anyhow!("invalid key: assembly"))?, + "GRCh37", + ) + .insert( + "species" + .parse() + .map_err(|_| anyhow::anyhow!("invalid key: species"))?, + "Homo sapiens", + ) + .build()?, + ); + } + + Ok(builder) +} + +/// Add contigs for GRCh38. +fn add_contigs_38(builder: vcf::header::Builder) -> Result { + use vcf::header::record::value::map::Contig; + use vcf::header::record::value::Map; + + let mut builder = builder; + + let specs: &[(&str, usize); 25] = &[ + ("chr1", 248956422), + ("chr2", 242193529), + ("chr3", 198295559), + ("chr4", 190214555), + ("chr5", 181538259), + ("chr6", 170805979), + ("chr7", 159345973), + ("chr8", 145138636), + ("chr9", 138394717), + ("chr10", 133797422), + ("chr11", 135086622), + ("chr12", 133275309), + ("chr13", 114364328), + ("chr14", 107043718), + ("chr15", 101991189), + ("chr16", 90338345), + ("chr17", 83257441), + ("chr18", 80373285), + ("chr19", 58617616), + ("chr20", 64444167), + ("chr21", 46709983), + ("chr22", 50818468), + ("chrX", 156040895), + ("chrY", 57227415), + ("chrM", 16569), + ]; + + for (contig, length) in specs { + builder = builder.add_contig( + contig + .parse() + .map_err(|_| anyhow::anyhow!("invalid contig: {}", contig))?, + Map::::builder() + .set_length(*length) + .insert( + "assembly" + .parse() + .map_err(|_| anyhow::anyhow!("invalid key: assembly"))?, + "GRCh38", + ) + .insert( + "species" + .parse() + .map_err(|_| anyhow::anyhow!("invalid key: species"))?, + "Homo sapiens", + ) + .build()?, + ); + } + + Ok(builder) +} + +/// Generate the output header from the input header. +pub fn build_output_header( + input_header: &vcf::Header, + pedigree: &Option, + genomebuild: GenomeRelease, + worker_version: &str, +) -> Result { + use vcf::header::record::value::{ + map::{info::Type, Filter, Format, Info}, + Map, + }; + use vcf::header::Number; + use vcf::record::genotypes::keys::key; + + let builder = vcf::Header::builder() + .add_filter("PASS", Map::::new("All filters passed")) + .add_info( + "gnomad_exomes_an".parse()?, + Map::::new( + Number::Count(1), + Type::Integer, + "Number of samples in gnomAD exomes", + ), + ) + .add_info( + "gnomad_exomes_hom".parse()?, + Map::::new( + Number::Count(1), + Type::Integer, + "Number of hom. alt. carriers in gnomAD exomes", + ), + ) + .add_info( + "gnomad_exomes_het".parse()?, + Map::::new( + Number::Count(1), + Type::Integer, + "Number of het. alt. carriers in gnomAD exomes", + ), + ) + .add_info( + "gnomad_exomes_hemi".parse()?, + Map::::new( + Number::Count(1), + Type::Integer, + "Number of hemi. alt. carriers in gnomAD exomes", + ), + ) + .add_info( + "gnomad_genomes_an".parse()?, + Map::::new( + Number::Count(1), + Type::Integer, + "Number of samples in gnomAD genomes", + ), + ) + .add_info( + "gnomad_genomes_hom".parse()?, + Map::::new( + Number::Count(1), + Type::Integer, + "Number of hom. alt. carriers in gnomAD genomes", + ), + ) + .add_info( + "gnomad_genomes_het".parse()?, + Map::::new( + Number::Count(1), + Type::Integer, + "Number of het. alt. carriers in gnomAD genomes", + ), + ) + .add_info( + "gnomad_genomes_hemi".parse()?, + Map::::new( + Number::Count(1), + Type::Integer, + "Number of hemi. alt. carriers in gnomAD genomes", + ), + ) + .add_info( + "helix_an".parse()?, + Map::::new( + Number::Count(1), + Type::Integer, + "Number of samples in HelixMtDb", + ), + ) + .add_info( + "helix_hom".parse()?, + Map::::new( + Number::Count(1), + Type::Integer, + "Number of hom. alt. carriers in HelixMtDb", + ), + ) + .add_info( + "helix_het".parse()?, + Map::::new( + Number::Count(1), + Type::Integer, + "Number of het. alt. carriers in HelixMtDb", + ), + ) + .add_info( + "ANN".parse()?, + Map::::new( + Number::Unknown, + Type::String, + "Functional annotations: 'Allele | Annotation | Annotation_Impact | \ + Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | \ + HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | \ + AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'", + ), + ) + .add_format(key::READ_DEPTHS, Map::::from(&key::READ_DEPTHS)) + .add_format(key::READ_DEPTH, Map::::from(&key::READ_DEPTH)) + .add_format( + key::CONDITIONAL_GENOTYPE_QUALITY, + Map::::from(&key::CONDITIONAL_GENOTYPE_QUALITY), + ) + .add_format(key::GENOTYPE, Map::::from(&key::GENOTYPE)) + .add_format(key::PHASE_SET, Map::::from(&key::PHASE_SET)); + + let mut builder = match genomebuild { + GenomeRelease::Grch37 => add_contigs_37(builder), + GenomeRelease::Grch38 => add_contigs_38(builder), + } + .map_err(|e| anyhow::anyhow!("problem adding contigs: {}", e))?; + + if let Some(pedigree) = pedigree { + let ped_idv = pedigree + .individuals + .iter() + .map(|(name, _)| name.clone()) + .collect::>(); + let input_idv = input_header + .sample_names() + .iter() + .cloned() + .collect::>(); + if !ped_idv.eq(&input_idv) { + anyhow::bail!( + "pedigree individuals = {:?} != input individuals: {:?}", + &ped_idv, + &input_idv + ) + } + + for name in input_header.sample_names() { + let i = pedigree + .individuals + .get(name) + .expect("checked equality above"); + if input_header.sample_names().contains(&i.name) { + builder = builder.add_sample_name(i.name.clone()); + } + + // Add SAMPLE entry. + builder = builder.insert( + "SAMPLE".parse()?, + noodles_vcf::header::record::Value::Map( + i.name.clone(), + Map::::builder() + .insert( + "Sex".parse()?, + mehari::annotate::strucvars::vcf_header::sex_str(i.sex), + ) + .insert( + "Disease".parse()?, + mehari::annotate::strucvars::vcf_header::disease_str(i.disease), + ) + .build()?, + ), + )?; + + // Add PEDIGREE entry. + let mut map_builder = Map::::builder(); + if let Some(father) = i.father.as_ref() { + map_builder = map_builder.insert("Father".parse()?, father.clone()); + } + if let Some(mother) = i.mother.as_ref() { + map_builder = map_builder.insert("Mother".parse()?, mother.clone()); + } + builder = builder.insert( + "PEDIGREE".parse()?, + noodles_vcf::header::record::Value::Map(i.name.clone(), map_builder.build()?), + )?; + } + } else { + for name in input_header.sample_names() { + builder = builder.add_sample_name(name.clone()); + } + } + + use vcf::header::record::value::map::Other; + + let orig_caller = VariantCaller::guess(input_header) + .ok_or_else(|| anyhow::anyhow!("unable to guess original variant caller"))?; + + let builder = builder.insert( + "x-varfish-version".parse()?, + vcf::header::record::Value::Map( + String::from("varfish-server-worker"), + Map::::builder() + .insert("Version".parse()?, worker_version) + .build()?, + ), + )?; + + let builder = match &orig_caller { + VariantCaller::GatkHaplotypeCaller { version } + | VariantCaller::GatkUnifiedGenotyper { version } + | VariantCaller::Dragen { version } => builder.insert( + "x-varfish-version".parse()?, + vcf::header::record::Value::Map( + String::from("orig-caller"), + Map::::builder() + .insert("Name".parse()?, orig_caller.name()) + .insert("Version".parse()?, version) + .build()?, + ), + )?, + VariantCaller::Other => builder.insert( + "x-varfish-version".parse()?, + vcf::header::record::Value::Map( + String::from("orig-caller"), + Map::::builder() + .insert("Name".parse()?, "Other") + .build()?, + ), + )?, + }; + + Ok(builder.build()) +} + +#[cfg(test)] +mod test { + use mehari::ped::PedigreeByName; + use rstest::rstest; + + use super::VariantCaller; + + macro_rules! set_snapshot_suffix { + ($($expr:expr),*) => { + let mut settings = insta::Settings::clone_current(); + settings.set_snapshot_suffix(format!($($expr,)*)); + let _guard = settings.bind_to_scope(); + } + } + + #[rstest] + #[case("tests/seqvars/ingest/example_dragen.07.021.624.3.10.4.vcf")] + #[case("tests/seqvars/ingest/example_dragen.07.021.624.3.10.9.vcf")] + #[case("tests/seqvars/ingest/example_gatk_hc.3.7-0.vcf")] + #[case("tests/seqvars/ingest/example_gatk_hc.4.4.0.0.vcf")] + fn variant_caller_guess(#[case] path: &str) -> Result<(), anyhow::Error> { + set_snapshot_suffix!("{}", path.split('/').last().unwrap()); + + let vcf_header = noodles_vcf::reader::Builder + .build_from_path(path)? + .read_header()?; + + insta::assert_yaml_snapshot!(VariantCaller::guess(&vcf_header)); + + Ok(()) + } + + #[rstest] + #[case("tests/seqvars/ingest/example_dragen.07.021.624.3.10.4.vcf")] + #[case("tests/seqvars/ingest/example_dragen.07.021.624.3.10.9.vcf")] + #[case("tests/seqvars/ingest/example_gatk_hc.3.7-0.vcf")] + #[case("tests/seqvars/ingest/example_gatk_hc.4.4.0.0.vcf")] + fn build_output_header_37(#[case] path: &str) -> Result<(), anyhow::Error> { + set_snapshot_suffix!("{}", path.split('/').last().unwrap()); + let tmpdir = temp_testdir::TempDir::default(); + + let pedigree = PedigreeByName::from_path(path.replace(".vcf", ".ped")).unwrap(); + + let input_vcf_header = noodles_vcf::reader::Builder + .build_from_path(path)? + .read_header()?; + let output_vcf_header = super::build_output_header( + &input_vcf_header, + &Some(pedigree), + crate::common::GenomeRelease::Grch37, + "x.y.z", + )?; + + let out_path = tmpdir.join("out.vcf"); + let out_path_str = out_path.to_str().expect("invalid path"); + { + noodles_vcf::writer::Writer::new(std::fs::File::create(out_path_str)?) + .write_header(&output_vcf_header)?; + } + + insta::assert_snapshot!(std::fs::read_to_string(out_path_str)?); + + Ok(()) + } + + #[rstest] + #[case("tests/seqvars/ingest/example_dragen.07.021.624.3.10.4.vcf")] + #[case("tests/seqvars/ingest/example_dragen.07.021.624.3.10.9.vcf")] + #[case("tests/seqvars/ingest/example_gatk_hc.3.7-0.vcf")] + #[case("tests/seqvars/ingest/example_gatk_hc.4.4.0.0.vcf")] + fn build_output_header_38(#[case] path: &str) -> Result<(), anyhow::Error> { + set_snapshot_suffix!("{}", path.split('/').last().unwrap()); + let tmpdir = temp_testdir::TempDir::default(); + + let pedigree = PedigreeByName::from_path(path.replace(".vcf", ".ped")).unwrap(); + + let input_vcf_header = noodles_vcf::reader::Builder + .build_from_path(path)? + .read_header()?; + let output_vcf_header = super::build_output_header( + &input_vcf_header, + &Some(pedigree), + crate::common::GenomeRelease::Grch38, + "x.y.z", + )?; + + let out_path = tmpdir.join("out.vcf"); + let out_path_str = out_path.to_str().expect("invalid path"); + { + noodles_vcf::writer::Writer::new(std::fs::File::create(out_path_str)?) + .write_header(&output_vcf_header)?; + } + + insta::assert_snapshot!(std::fs::read_to_string(out_path_str)?); + + Ok(()) + } +} diff --git a/src/seqvars/ingest/mod.rs b/src/seqvars/ingest/mod.rs new file mode 100644 index 00000000..27a67322 --- /dev/null +++ b/src/seqvars/ingest/mod.rs @@ -0,0 +1,563 @@ +//! Implementation of `seqvars ingest` subcommand. + +use std::sync::{Arc, OnceLock}; + +use crate::common::{self, open_read_maybe_gz, open_write_maybe_gz, GenomeRelease}; +use mehari::annotate::seqvars::provider::MehariProvider; +use noodles_vcf as vcf; +use thousands::Separable; + +pub mod header; + +/// Command line arguments for `seqvars ingest` subcommand. +#[derive(Debug, clap::Parser)] +#[command(author, version, about = "ingest sequence variant VCF", long_about = None)] +pub struct Args { + /// Maximal number of variants to write out; optional. + #[clap(long)] + pub max_var_count: Option, + /// The path to the mehari database. + #[clap(long)] + pub path_mehari_db: String, + /// The assumed genome build. + #[clap(long)] + pub genomebuild: GenomeRelease, + /// Path to the pedigree file. + #[clap(long)] + pub path_ped: String, + /// Path to input file. + #[clap(long)] + pub path_in: String, + /// Path to output file. + #[clap(long)] + pub path_out: String, +} + +/// Return the version of the `varfish-server-worker` crate and `x.y.z` in tests. +fn worker_version() -> &'static str { + if cfg!(test) { + "x.y.z" + } else { + env!("CARGO_PKG_VERSION") + } +} + +/// Return path component fo rth egiven assembly. +pub fn path_component(genomebuild: GenomeRelease) -> &'static str { + match genomebuild { + GenomeRelease::Grch37 => "grch37", + GenomeRelease::Grch38 => "grch38", + } +} + +/// Known keys information and logic for `FORMAT`. +#[derive(Debug)] +struct KnownFormatKeys { + /// The keys that will be written to the output. + output_keys: Vec, + /// The keys that are known from the input keys. + known_keys: Vec, + /// Mapping from known to output keys where it is not identity + known_to_output_map: std::collections::HashMap< + vcf::record::genotypes::keys::Key, + vcf::record::genotypes::keys::Key, + >, +} + +impl Default for KnownFormatKeys { + /// Constructor. + fn default() -> Self { + Self { + output_keys: vec![ + vcf::record::genotypes::keys::key::GENOTYPE, // GT + vcf::record::genotypes::keys::key::CONDITIONAL_GENOTYPE_QUALITY, // GQ + vcf::record::genotypes::keys::key::READ_DEPTH, // DP + vcf::record::genotypes::keys::key::READ_DEPTHS, // AD + vcf::record::genotypes::keys::key::PHASE_SET, // PS + ], + known_keys: vec![ + vcf::record::genotypes::keys::key::GENOTYPE, + vcf::record::genotypes::keys::key::CONDITIONAL_GENOTYPE_QUALITY, + vcf::record::genotypes::keys::key::READ_DEPTH, + vcf::record::genotypes::keys::key::READ_DEPTHS, + vcf::record::genotypes::keys::key::PHASE_SET, // PS + "SQ".parse().expect("invalid key: SQ"), // written as AD + ], + known_to_output_map: vec![( + "SQ".parse().expect("invalid key: SQ"), + vcf::record::genotypes::keys::key::CONDITIONAL_GENOTYPE_QUALITY, + )] + .into_iter() + .collect(), + } + } +} + +impl KnownFormatKeys { + /// Map from known to output key. + pub fn known_to_output( + &self, + key: &vcf::record::genotypes::keys::Key, + ) -> vcf::record::genotypes::keys::Key { + self.known_to_output_map.get(key).unwrap_or(key).clone() + } +} + +/// The known `FORMAT` keys. +static KNOWN_FORMAT_KEYS: OnceLock = OnceLock::new(); + +/// Transform the ``FORMAT`` key if known. +fn transform_format_value( + value: &Option<&vcf::record::genotypes::sample::Value>, + key: &vcf::record::genotypes::keys::Key, + allele_no: usize, +) -> Option> { + if let Some(value) = value { + Some(Some(match key.as_ref() { + "AD" => { + // Only write out current allele as AD. + match *value { + vcf::record::genotypes::sample::Value::Array( + vcf::record::genotypes::sample::value::Array::Integer(ad_values), + ) => vcf::record::genotypes::sample::Value::Integer( + ad_values[allele_no].expect("SQ should be integer value"), + ), + _ => return None, // unreachable!("FORMAT/AD must be array of integer"), + } + } + "SQ" => { + // SQ is written as AD. + match *value { + vcf::record::genotypes::sample::Value::Float(sq_value) => { + vcf::record::genotypes::sample::Value::Float(*sq_value) + } + vcf::record::genotypes::sample::Value::Array( + vcf::record::genotypes::sample::value::Array::Float(sq_values), + ) => vcf::record::genotypes::sample::Value::Float( + sq_values[allele_no].expect("SQ should be float value"), + ), + _ => return None, // unreachable!("FORMAT/PS must be integer"), + } + } + _ => return None, // unreachable!("unknown key: {:?}", key), + })) + } else { + Some(None) + } +} + +/// Copy the `FORMAT/GQ` fields for all samples. +/// +/// The implementation assumes that there are no duplicates in the output keys when mapped +/// from input keys. +fn copy_format( + input_record: &vcf::Record, + builder: vcf::record::Builder, + idx_output_to_input: &[usize], + allele_no: usize, + known_format_keys: &KnownFormatKeys, +) -> Result { + let keys_from_input_known = input_record + .genotypes() + .keys() + .iter() + .filter(|k| known_format_keys.known_keys.contains(*k)) + .cloned() + .collect::>(); + let output_keys = keys_from_input_known + .iter() + .map(|k| known_format_keys.known_to_output(k).clone()) + .collect::>(); + + let values = idx_output_to_input + .iter() + .copied() + .map(|input_idx| { + let sample = input_record + .genotypes() + .get_index(input_idx) + .expect("input_idx must be valid here"); + keys_from_input_known + .iter() + .map(|key| { + let input_value = sample.get(key).expect("key must be valid"); + if let Some(value) = transform_format_value(&input_value, key, allele_no) { + value + } else if known_format_keys.output_keys.contains(key) { + input_value.cloned() + } else { + unreachable!("don't know how to handle key: {:?}", key) + } + }) + .collect::>() + }) + .collect::>(); + + let genotypes = vcf::record::Genotypes::new( + vcf::record::genotypes::Keys::try_from(output_keys).expect("invalid keys"), + values, + ); + + Ok(builder.set_genotypes(genotypes)) +} + +/// Process the variants from `input_reader` to `output_writer`. +fn process_variants( + output_writer: &mut vcf::Writer, + input_reader: &mut vcf::Reader, + output_header: &vcf::Header, + input_header: &vcf::Header, + args: &Args, +) -> Result<(), anyhow::Error> +where + R: std::io::BufRead, + W: std::io::Write, +{ + // Open the frequency RocksDB database in read only mode. + tracing::info!("Opening frequency database"); + let rocksdb_path = format!( + "{}/{}/seqvars/freqs/rocksdb", + &args.path_mehari_db, + path_component(args.genomebuild) + ); + tracing::debug!("RocksDB path = {}", &rocksdb_path); + let options = rocksdb::Options::default(); + let db_freq = rocksdb::DB::open_cf_for_read_only( + &options, + &rocksdb_path, + ["meta", "autosomal", "gonosomal", "mitochondrial"], + false, + )?; + + let cf_autosomal = db_freq.cf_handle("autosomal").unwrap(); + let cf_gonosomal = db_freq.cf_handle("gonosomal").unwrap(); + let cf_mtdna = db_freq.cf_handle("mitochondrial").unwrap(); + + // Open the ClinVar RocksDB database in read only mode. + tracing::info!("Opening ClinVar database"); + let rocksdb_path = format!( + "{}/{}/seqvars/clinvar/rocksdb", + &args.path_mehari_db, + path_component(args.genomebuild) + ); + tracing::debug!("RocksDB path = {}", &rocksdb_path); + let options = rocksdb::Options::default(); + let db_clinvar = + rocksdb::DB::open_cf_for_read_only(&options, &rocksdb_path, ["meta", "clinvar"], false)?; + + let cf_clinvar = db_clinvar.cf_handle("clinvar").unwrap(); + + // Open the serialized transcripts. + tracing::info!("Opening transcript database"); + let tx_db = mehari::annotate::seqvars::load_tx_db(&format!( + "{}/{}/txs.bin.zst", + &args.path_mehari_db, + path_component(args.genomebuild) + ))?; + tracing::info!("Building transcript interval trees ..."); + let assembly = if args.genomebuild == GenomeRelease::Grch37 { + hgvs::static_data::Assembly::Grch37p10 + } else { + hgvs::static_data::Assembly::Grch38 + }; + let provider = Arc::new(MehariProvider::new(tx_db, assembly)); + let predictor = mehari::annotate::seqvars::csq::ConsequencePredictor::new(provider, assembly); + tracing::info!("... done building transcript interval trees"); + + // Build mapping from output sample index to input sample index. + let idx_output_to_input = { + let output_sample_to_idx = output_header + .sample_names() + .iter() + .enumerate() + .map(|(idx, name)| (name, idx)) + .collect::>(); + let mut res = vec![usize::MAX; output_header.sample_names().len()]; + for (input_idx, sample) in input_header.sample_names().iter().enumerate() { + res[output_sample_to_idx[sample]] = input_idx; + } + res + }; + + // Read through input file, construct output records, and annotate these. + let start = std::time::Instant::now(); + let mut prev = std::time::Instant::now(); + let mut total_written = 0usize; + let mut records = input_reader.records(input_header); + let known_format_keys = KNOWN_FORMAT_KEYS.get_or_init(Default::default); + loop { + if let Some(input_record) = records.next() { + let input_record = input_record?; + + for (allele_no, alt_allele) in input_record.alternate_bases().iter().enumerate() { + // Construct record with first few fields describing one variant allele. + let builder = vcf::Record::builder() + .set_chromosome(input_record.chromosome().clone()) + .set_position(input_record.position()) + .set_reference_bases(input_record.reference_bases().clone()) + .set_alternate_bases(vcf::record::AlternateBases::from(vec![ + alt_allele.clone() + ])); + + // Copy over the well-known FORMAT fields and construct output record. + let builder = copy_format( + &input_record, + builder, + &idx_output_to_input, + allele_no, + known_format_keys, + )?; + + let mut output_record = builder.build()?; + + // Obtain annonars variant key from current allele for RocksDB lookup. + let vcf_var = annonars::common::keys::Var::from_vcf_allele(&output_record, 0); + + // Skip records with a deletion as alternative allele. + if vcf_var.alternative == "*" { + continue; + } + + if prev.elapsed().as_secs() >= 60 { + tracing::info!("at {:?}", &vcf_var); + prev = std::time::Instant::now(); + } + + // Only attempt lookups into RocksDB for canonical contigs. + if annonars::common::cli::is_canonical(vcf_var.chrom.as_str()) { + // Build key for RocksDB database from `vcf_var`. + let key: Vec = vcf_var.clone().into(); + + // Annotate with frequency. + if mehari::annotate::seqvars::CHROM_AUTO.contains(vcf_var.chrom.as_str()) { + mehari::annotate::seqvars::annotate_record_auto( + &db_freq, + &cf_autosomal, + &key, + &mut output_record, + )?; + } else if mehari::annotate::seqvars::CHROM_XY.contains(vcf_var.chrom.as_str()) { + mehari::annotate::seqvars::annotate_record_xy( + &db_freq, + &cf_gonosomal, + &key, + &mut output_record, + )?; + } else if mehari::annotate::seqvars::CHROM_MT.contains(vcf_var.chrom.as_str()) { + mehari::annotate::seqvars::annotate_record_mt( + &db_freq, + &cf_mtdna, + &key, + &mut output_record, + )?; + } else { + tracing::trace!( + "Record @{:?} on non-canonical chromosome, skipping.", + &vcf_var + ); + } + + // Annotate with ClinVar information. + mehari::annotate::seqvars::annotate_record_clinvar( + &db_clinvar, + &cf_clinvar, + &key, + &mut output_record, + )?; + } + + let annonars::common::keys::Var { + chrom, + pos, + reference, + alternative, + } = vcf_var; + + // Annotate with variant effect. + if let Some(ann_fields) = + predictor.predict(&mehari::annotate::seqvars::csq::VcfVariant { + chromosome: chrom, + position: pos, + reference, + alternative, + })? + { + if !ann_fields.is_empty() { + output_record.info_mut().insert( + "ANN".parse()?, + Some(vcf::record::info::field::Value::Array( + vcf::record::info::field::value::Array::String( + ann_fields.iter().map(|ann| Some(ann.to_string())).collect(), + ), + )), + ); + } + } + + // Write out the record. + output_writer.write_record(output_header, &output_record)?; + total_written += 1; + } + } else { + break; // all done + } + + if let Some(max_var_count) = args.max_var_count { + if total_written >= max_var_count { + tracing::warn!( + "Stopping after {} records as requested by --max-var-count", + total_written + ); + break; + } + } + } + tracing::info!( + "... annotated {} records in {:?}", + total_written.separate_with_commas(), + start.elapsed() + ); + + Ok(()) +} + +/// Main entry point for `seqvars ingest` sub command. +pub fn run(args_common: &crate::common::Args, args: &Args) -> Result<(), anyhow::Error> { + let before_anything = std::time::Instant::now(); + tracing::info!("args_common = {:#?}", &args_common); + tracing::info!("args = {:#?}", &args); + + common::trace_rss_now(); + + tracing::info!("loading pedigree..."); + let pedigree = mehari::ped::PedigreeByName::from_path(&args.path_ped) + .map_err(|e| anyhow::anyhow!("problem parsing PED file: {}", e))?; + tracing::info!("pedigre = {:#?}", &pedigree); + + tracing::info!("opening input file..."); + let mut input_reader = { + vcf::reader::Builder + .build_from_reader(open_read_maybe_gz(&args.path_in)?) + .map_err(|e| anyhow::anyhow!("could not build VCF reader: {}", e))? + }; + + tracing::info!("processing header..."); + let input_header = input_reader + .read_header() + .map_err(|e| anyhow::anyhow!("problem reading VCF header: {}", e))?; + let output_header = header::build_output_header( + &input_header, + &Some(pedigree), + args.genomebuild, + worker_version(), + ) + .map_err(|e| anyhow::anyhow!("problem building output header: {}", e))?; + + let mut output_writer = { vcf::writer::Writer::new(open_write_maybe_gz(&args.path_out)?) }; + output_writer + .write_header(&output_header) + .map_err(|e| anyhow::anyhow!("problem writing header: {}", e))?; + + process_variants( + &mut output_writer, + &mut input_reader, + &output_header, + &input_header, + args, + )?; + + tracing::info!( + "All of `seqvars ingest` completed in {:?}", + before_anything.elapsed() + ); + Ok(()) +} + +#[cfg(test)] +mod test { + use std::io::Read; + + use rstest::rstest; + + use crate::common::GenomeRelease; + + macro_rules! set_snapshot_suffix { + ($($expr:expr),*) => { + let mut settings = insta::Settings::clone_current(); + settings.set_snapshot_suffix(format!($($expr,)*)); + let _guard = settings.bind_to_scope(); + } + } + + #[rstest] + #[case("tests/seqvars/ingest/example_dragen.07.021.624.3.10.4.vcf")] + #[case("tests/seqvars/ingest/example_dragen.07.021.624.3.10.9.vcf")] + #[case("tests/seqvars/ingest/example_gatk_hc.3.7-0.vcf")] + #[case("tests/seqvars/ingest/example_gatk_hc.4.4.0.0.vcf")] + #[case("tests/seqvars/ingest/NA12878_dragen.vcf")] + #[case("tests/seqvars/ingest/Case_1.vcf")] + fn result_snapshot_test(#[case] path: &str) -> Result<(), anyhow::Error> { + set_snapshot_suffix!("{}", path.split('/').last().unwrap().replace('.', "_")); + + let tmpdir = temp_testdir::TempDir::default(); + + let args_common = Default::default(); + let args = super::Args { + max_var_count: None, + path_mehari_db: "tests/seqvars/ingest/db".into(), + path_ped: path.replace(".vcf", ".ped"), + genomebuild: GenomeRelease::Grch37, + path_in: path.into(), + path_out: tmpdir + .join("out.vcf") + .to_str() + .expect("invalid path") + .into(), + }; + super::run(&args_common, &args)?; + + insta::assert_snapshot!(std::fs::read_to_string(&args.path_out)?); + + Ok(()) + } + + fn read_to_bytes

(path: P) -> Result, anyhow::Error> + where + P: AsRef, + { + let mut f = std::fs::File::open(&path).expect("no file found"); + let metadata = std::fs::metadata(&path).expect("unable to read metadata"); + let mut buffer = vec![0; metadata.len() as usize]; + f.read_exact(&mut buffer).expect("buffer overflow"); + Ok(buffer) + } + + #[test] + fn result_snapshot_test_gz() -> Result<(), anyhow::Error> { + let tmpdir = temp_testdir::TempDir::default(); + + let path_in: String = "tests/seqvars/ingest/NA12878_dragen.vcf.gz".into(); + let path_ped = path_in.replace(".vcf.gz", ".ped"); + let path_out = tmpdir + .join("out.vcf.gz") + .to_str() + .expect("invalid path") + .into(); + let args_common = Default::default(); + let args = super::Args { + max_var_count: None, + path_mehari_db: "tests/seqvars/ingest/db".into(), + path_ped, + genomebuild: GenomeRelease::Grch37, + path_in, + path_out, + }; + super::run(&args_common, &args)?; + + let mut buffer = Vec::new(); + hxdmp::hexdump(&read_to_bytes(&args.path_out)?, &mut buffer)?; + insta::assert_snapshot!(String::from_utf8_lossy(&buffer)); + + Ok(()) + } +} diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_dragen.07.021.624.3.10.4.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_dragen.07.021.624.3.10.4.vcf.snap new file mode 100644 index 00000000..bd8cddd1 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_dragen.07.021.624.3.10.4.vcf.snap @@ -0,0 +1,54 @@ +--- +source: src/seqvars/ingest/header.rs +expression: "std::fs::read_to_string(out_path_str)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##SAMPLE= +##PEDIGREE= +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_dragen.07.021.624.3.10.9.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_dragen.07.021.624.3.10.9.vcf.snap new file mode 100644 index 00000000..0ac20822 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_dragen.07.021.624.3.10.9.vcf.snap @@ -0,0 +1,54 @@ +--- +source: src/seqvars/ingest/header.rs +expression: "std::fs::read_to_string(out_path_str)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##SAMPLE= +##PEDIGREE= +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CASE + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_gatk_hc.3.7-0.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_gatk_hc.3.7-0.vcf.snap new file mode 100644 index 00000000..6db95979 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_gatk_hc.3.7-0.vcf.snap @@ -0,0 +1,58 @@ +--- +source: src/seqvars/ingest/header.rs +expression: "std::fs::read_to_string(out_path_str)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##SAMPLE= +##SAMPLE= +##SAMPLE= +##PEDIGREE= +##PEDIGREE= +##PEDIGREE= +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Case_1_father-N1-DNA1-WGS1 Case_1_index-N1-DNA1-WGS1 Case_1_mother-N1-DNA1-WGS1 + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_gatk_hc.4.4.0.0.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_gatk_hc.4.4.0.0.vcf.snap new file mode 100644 index 00000000..cb817ee3 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_37@example_gatk_hc.4.4.0.0.vcf.snap @@ -0,0 +1,54 @@ +--- +source: src/seqvars/ingest/header.rs +expression: "std::fs::read_to_string(out_path_str)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##SAMPLE= +##PEDIGREE= +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CASE + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.4.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.4.vcf.snap new file mode 100644 index 00000000..4cf1ccfd --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.4.vcf.snap @@ -0,0 +1,54 @@ +--- +source: src/seqvars/ingest/header.rs +expression: "std::fs::read_to_string(out_path_str)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##SAMPLE= +##PEDIGREE= +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.9.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.9.vcf.snap new file mode 100644 index 00000000..54721644 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_dragen.07.021.624.3.10.9.vcf.snap @@ -0,0 +1,54 @@ +--- +source: src/seqvars/ingest/header.rs +expression: "std::fs::read_to_string(out_path_str)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##SAMPLE= +##PEDIGREE= +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CASE + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.3.7-0.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.3.7-0.vcf.snap new file mode 100644 index 00000000..e1a92636 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.3.7-0.vcf.snap @@ -0,0 +1,58 @@ +--- +source: src/seqvars/ingest/header.rs +expression: "std::fs::read_to_string(out_path_str)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##SAMPLE= +##SAMPLE= +##SAMPLE= +##PEDIGREE= +##PEDIGREE= +##PEDIGREE= +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Case_1_father-N1-DNA1-WGS1 Case_1_index-N1-DNA1-WGS1 Case_1_mother-N1-DNA1-WGS1 + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.4.4.0.0.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.4.4.0.0.vcf.snap new file mode 100644 index 00000000..6944a30d --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_38@example_gatk_hc.4.4.0.0.vcf.snap @@ -0,0 +1,54 @@ +--- +source: src/seqvars/ingest/header.rs +expression: "std::fs::read_to_string(out_path_str)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##SAMPLE= +##PEDIGREE= +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CASE + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_ped.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_ped.snap new file mode 100644 index 00000000..16d943b7 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__build_output_header_ped.snap @@ -0,0 +1,58 @@ +--- +source: src/seqvars/ingest/header.rs +expression: "std::fs::read_to_string(out_path_str)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##SAMPLE= +##SAMPLE= +##SAMPLE= +##PEDIGREE= +##PEDIGREE= +##PEDIGREE= +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Case_1_father-N1-DNA1-WGS1 Case_1_index-N1-DNA1-WGS1 Case_1_mother-N1-DNA1-WGS1 + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_dragen.07.021.624.3.10.4.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_dragen.07.021.624.3.10.4.vcf.snap new file mode 100644 index 00000000..0df41bd3 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_dragen.07.021.624.3.10.4.vcf.snap @@ -0,0 +1,7 @@ +--- +source: src/seqvars/ingest/header.rs +expression: "VariantCaller::guess(&vcf_header)" +--- +Dragen: + version: "SW: 07.021.624.3.10.4, HW: 07.021.624" + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_dragen.07.021.624.3.10.9.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_dragen.07.021.624.3.10.9.vcf.snap new file mode 100644 index 00000000..5089a957 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_dragen.07.021.624.3.10.9.vcf.snap @@ -0,0 +1,7 @@ +--- +source: src/seqvars/ingest/header.rs +expression: "VariantCaller::guess(&vcf_header)" +--- +Dragen: + version: "SW: 07.021.624.3.10.9, HW: 07.021.624" + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_gatk_hc.3.7-0.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_gatk_hc.3.7-0.vcf.snap new file mode 100644 index 00000000..d6f9fb36 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_gatk_hc.3.7-0.vcf.snap @@ -0,0 +1,7 @@ +--- +source: src/seqvars/ingest/header.rs +expression: "VariantCaller::guess(&vcf_header)" +--- +GatkHaplotypeCaller: + version: 3.7-0-gcfedb67 + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_gatk_hc.4.4.0.0.vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_gatk_hc.4.4.0.0.vcf.snap new file mode 100644 index 00000000..aeddbb48 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__header__test__variant_caller_guess@example_gatk_hc.4.4.0.0.vcf.snap @@ -0,0 +1,7 @@ +--- +source: src/seqvars/ingest/header.rs +expression: "VariantCaller::guess(&vcf_header)" +--- +GatkHaplotypeCaller: + version: 4.4.0.0 + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@Case_1_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@Case_1_vcf.snap new file mode 100644 index 00000000..a79c8c31 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@Case_1_vcf.snap @@ -0,0 +1,121 @@ +--- +source: src/seqvars/ingest/mod.rs +expression: "std::fs::read_to_string(&args.path_out)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##SAMPLE= +##SAMPLE= +##SAMPLE= +##PEDIGREE= +##PEDIGREE= +##PEDIGREE= +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Case_1_father-N1-DNA1-WGS1 Case_1_index-N1-DNA1-WGS1 Case_1_mother-N1-DNA1-WGS1 +17 41249263 . G A . . gnomad_exomes_an=31398;gnomad_exomes_hom=0;gnomad_exomes_het=56;gnomad_genomes_an=251304;gnomad_genomes_hom=0;gnomad_genomes_het=369;clinvar_clinsig=benign;clinvar_rcv=RCV001353617;ANN=A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/23|c.591C>T|p.C197=|704/7088|591/5592|197/1864|44|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/22|c.450C>T|p.C150=|644/7028|450/5451|150/1817|44|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/22|c.591C>T|p.C197=|698/3696|591/2100|197/700|44|,A|splice_region_variant&synonymous_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/24|c.591C>T|p.C197=|704/7151|591/5655|197/1885|44| GT:AD:DP:GQ 0/0:52:52:99 0/0:46:46:99 0/1:21:42:99 +17 41252332 . T C . . ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-435A>G|p.?|555/7088|442/5592||-434|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-435A>G|p.?|495/7028|301/5451||-434|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-435A>G|p.?|549/3696|442/2100||-434|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-435A>G|p.?|555/7151|442/5655||-434| GT:AD:DP:GQ 0/0:25:25:75 0/1:14:28:99 0/1:19:40:99 +17 41252691 . ATATAAT A . . gnomad_exomes_an=2368;gnomad_exomes_hom=10;gnomad_exomes_het=80;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-800_442-795delATTATA|p.?|555/7088|442/5592||-794|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-795delATTATA|p.?|495/7028|301/5451||-794|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-795delATTATA|p.?|549/3696|442/2100||-794|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-795delATTATA|p.?|555/7151|442/5655||-794| GT:AD:DP:GQ 0/0:9:9:27 0/1:4:14:99 0/1:12:23:99 +17 41252693 . ATAAT A . . gnomad_exomes_an=3866;gnomad_exomes_hom=244;gnomad_exomes_het=618;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-800_442-797delATTA|p.?|555/7088|442/5592||-796|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-797delATTA|p.?|495/7028|301/5451||-796|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-797delATTA|p.?|549/3696|442/2100||-796|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-797delATTA|p.?|555/7151|442/5655||-796| GT:AD:DP:GQ 0/0:9:9:27 0/0:14:14:42 0/1:11:22:99 +17 41252695 . AAT A . . gnomad_exomes_an=5066;gnomad_exomes_hom=546;gnomad_exomes_het=795;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-800_442-799delAT|p.?|555/7088|442/5592||-798|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-800_301-799delAT|p.?|495/7028|301/5451||-798|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-800_442-799delAT|p.?|549/3696|442/2100||-798|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-800_442-799delAT|p.?|555/7151|442/5655||-798| GT:AD:DP:GQ 0/1:3:9:79 0/0:14:14:42 0/0:22:22:66 +17 41252696 . A T . . gnomad_exomes_an=4200;gnomad_exomes_hom=29;gnomad_exomes_het=334;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-799T>A|p.?|555/7088|442/5592||-798|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-799T>A|p.?|495/7028|301/5451||-798|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-799T>A|p.?|549/3696|442/2100||-798|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-799T>A|p.?|555/7151|442/5655||-798| GT:AD:DP:GQ 0/1:6:9:78 0/1:10:14:98 0/0:22:22:67 +17 41252697 . A AT . . ANN=AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-801_442-800insA|p.?|555/7088|442/5592||-800|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insA|p.?|495/7028|301/5451||-800|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insA|p.?|549/3696|442/2100||-800|,AT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insA|p.?|555/7151|442/5655||-800| GT:AD:DP:GQ 1/1:0:45:99 1/2:0:33:99 1/2:1:33:99 +17 41252697 . A ATT . . ANN=ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-801_442-800insAA|p.?|555/7088|442/5592||-800|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-801_301-800insAA|p.?|495/7028|301/5451||-800|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-801_442-800insAA|p.?|549/3696|442/2100||-800|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-801_442-800insAA|p.?|555/7151|442/5655||-800| GT:AD:DP:GQ 1/1:45:45:99 1/2:17:33:99 1/2:11:33:99 +17 41254393 . G T . . gnomad_exomes_an=1936;gnomad_exomes_hom=0;gnomad_exomes_het=167;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1746C>A|p.?|554/7088|441/5592||1745|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1746C>A|p.?|494/7028|300/5451||1745|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1746C>A|p.?|548/3696|441/2100||1745|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1746C>A|p.?|554/7151|441/5655||1745| GT:AD:DP:GQ 0/1:29:37:66 ./.:.:.:. 0/0:32:35:47 +17 41273700 . C CA . . ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2333_80+2334insT|p.?|193/7088|80/5592||2333|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2333_-8+2334insT|p.?|187/7028|-8/5451||2333|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2333_80+2334insT|p.?|187/3696|80/2100||2333|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2333_80+2334insT|p.?|193/7151|80/5655||2333| GT:AD:DP:GQ 0/0:14:14:42 0/0:6:7:10 0/1:5:10:65 +MT 73 . A G . . . GT:AD:DP:GQ 0/0:3975:3975:99 1/1:0:2871:99 1/1:0:3320:99 +MT 119 . T C . . . GT:AD:DP:GQ 0/0:5417:5418:99 1/1:0:4039:99 1/1:1:4113:99 +MT 189 . A G . . . GT:AD:DP:GQ 0/0:3069:3069:99 1/1:0:1721:99 1/1:0:2204:99 +MT 195 . T C . . . GT:AD:DP:GQ 0/0:2599:2599:99 1/1:0:1592:99 1/1:0:1815:99 +MT 204 . T C . . . GT:AD:DP:GQ 0/0:2180:2180:99 1/1:0:1424:99 1/1:0:1304:99 +MT 207 . G A . . . GT:AD:DP:GQ 0/0:2115:2115:99 1/1:0:1408:99 1/1:0:1277:99 +MT 263 . A G . . . GT:AD:DP:GQ 1/1:0:1288:99 1/1:0:1204:99 1/1:0:1031:99 +MT 302 . A ACC . . . GT:AD:DP:GQ 0/1:157:844:99 0/0:1005:1011:99 0/0:800:803:99 +MT 310 . T TC . . . GT:AD:DP:GQ 1/1:0:1035:99 1/1:0:1411:99 1/1:1:1091:99 +MT 477 . T C . . . GT:AD:DP:GQ 1/1:4:2133:99 0/0:2266:2267:99 0/0:1725:1725:99 +MT 709 . G A . . . GT:AD:DP:GQ 0/0:2494:2494:99 1/1:0:2186:99 1/1:1:1814:99 +MT 750 . A G . . . GT:AD:DP:GQ 1/1:0:2757:99 1/1:0:2392:99 1/1:0:1621:99 +MT 879 . T C . . . GT:AD:DP:GQ 0/0:2853:2853:99 0/0:2784:2784:99 0/1:1351:1898:99 +MT 1243 . T C . . . GT:AD:DP:GQ 0/0:2674:2675:99 1/1:0:2198:99 1/1:0:1655:99 +MT 1438 . A G . . . GT:AD:DP:GQ 1/1:0:3815:99 1/1:0:3653:99 1/1:0:2900:99 +MT 1824 . T C . . . GT:AD:DP:GQ 1/1:0:2668:99 0/0:2409:2409:99 0/0:1752:1752:99 +MT 2633 . A G . . . GT:AD:DP:GQ 0/0:2535:2535:99 0/1:1648:2409:99 0/0:2269:2269:99 +MT 2706 . A G . . . GT:AD:DP:GQ 0/0:3200:3200:99 1/1:0:2847:99 1/1:0:2020:99 +MT 3010 . G A . . . GT:AD:DP:GQ 1/1:0:2841:99 0/0:2385:2385:99 0/0:1685:1685:99 +MT 3505 . A G . . . GT:AD:DP:GQ 0/0:2580:2594:99 1/1:0:2363:99 1/1:0:1664:99 +MT 3784 . T C . . . GT:AD:DP:GQ 0/1:480:2936:99 0/0:2504:2504:99 0/0:1991:1991:99 +MT 4769 . A G . . . GT:AD:DP:GQ 1/1:0:2689:99 1/1:0:2549:99 1/1:0:2108:99 +MT 5046 . G A . . . GT:AD:DP:GQ 0/0:2876:2878:99 1/1:0:2466:99 1/1:0:1661:99 +MT 5460 . G A . . . GT:AD:DP:GQ 0/0:2905:2907:99 1/1:0:2759:99 1/1:2:1970:99 +MT 7028 . C T . . . GT:AD:DP:GQ 0/0:2577:2580:99 1/1:2:2203:99 1/1:1:1946:99 +MT 7864 . C T . . . GT:AD:DP:GQ 0/0:3588:3589:99 1/1:0:3465:99 1/1:0:2746:99 +MT 8170 . A G . . . GT:AD:DP:GQ 0/0:2051:2052:99 1/1:0:2257:99 1/1:0:1774:99 +MT 8251 . G A . . . GT:AD:DP:GQ 0/0:2360:2360:99 1/1:0:2317:99 1/1:1:1625:99 +MT 8860 . A G . . . GT:AD:DP:GQ 1/1:0:3278:99 1/1:0:3088:99 1/1:0:2241:99 +MT 8994 . G A . . . GT:AD:DP:GQ 0/0:2793:2793:99 1/1:0:2368:99 1/1:1:1918:99 +MT 9007 . A G . . . GT:AD:DP:GQ 1/1:0:2959:99 0/0:2442:2442:99 0/0:1735:1735:99 +MT 9150 . A G . . . GT:AD:DP:GQ 1/1:0:3163:99 0/0:3538:3538:99 0/0:2767:2767:99 +MT 9380 . G A . . . GT:AD:DP:GQ 1/1:1:3321:99 0/0:3222:3222:99 0/0:2547:2547:99 +MT 10097 . A G . . . GT:AD:DP:GQ 0/0:2660:2660:99 0/1:1680:2188:99 0/0:1851:1851:99 +MT 11204 . T C . . . GT:AD:DP:GQ 0/0:3168:3173:99 1/1:0:2922:99 1/1:0:2418:99 +MT 11674 . C T . . . GT:AD:DP:GQ 0/0:2890:2890:99 1/1:0:2666:99 1/1:1:2180:99 +MT 11719 . G A . . . GT:AD:DP:GQ 0/0:3339:3341:99 1/1:0:3052:99 1/1:0:2203:99 +MT 11947 . A G . . . GT:AD:DP:GQ 0/0:2579:2581:99 1/1:0:2273:99 1/1:0:1804:99 +MT 12414 . T C . . . GT:AD:DP:GQ 0/0:2852:2855:99 1/1:1:2546:99 1/1:0:1733:99 +MT 12648 . A G . . . GT:AD:DP:GQ 0/0:1812:1813:99 1/1:2:1664:99 1/1:4:1781:99 +MT 12705 . C T . . . GT:AD:DP:GQ 0/0:2359:2369:99 1/1:1:2138:99 1/1:1:1622:99 +MT 13406 . G A . . . GT:AD:DP:GQ 0/0:2539:2540:99 0/0:2216:2216:99 0/1:1224:1957:99 +MT 13611 . A G . . . GT:AD:DP:GQ 0/0:3838:3840:99 1/1:0:3717:99 1/1:1:2835:99 +MT 13928 . G C . . . GT:AD:DP:GQ 0/0:2947:2947:99 1/1:0:2700:99 1/1:0:1880:99 +MT 14148 . A G . . . GT:AD:DP:GQ 0/0:3019:3021:99 1/1:0:2820:99 1/1:0:1962:99 +MT 14766 . C T . . . GT:AD:DP:GQ 0/0:3318:3321:99 1/1:2:3113:99 1/1:3:2358:99 +MT 15326 . A G . . . GT:AD:DP:GQ 1/1:0:3716:99 1/1:0:3560:99 1/1:0:2690:99 +MT 15884 . G C . . . GT:AD:DP:GQ 0/0:3595:3596:99 1/1:0:3167:99 1/1:1:2734:99 +MT 16184 . C T . . . GT:AD:DP:GQ 0/0:1406:1407:99 1/1:0:1969:99 1/1:0:1478:99 +MT 16223 . C T . . . GT:AD:DP:GQ 0/0:1405:1406:99 1/1:0:2018:99 1/1:0:1472:99 +MT 16263 . T C . . . GT:AD:DP:GQ 1/1:2:1478:99 0/0:1994:1994:99 0/0:1475:1475:99 +MT 16292 . C T . . . GT:AD:DP:GQ 0/0:1652:1652:99 1/1:1:1914:99 1/1:0:1476:99 +MT 16519 . T C . . . GT:AD:DP:GQ 1/1:0:1759:99 1/1:0:4094:99 1/1:0:1744:99 + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@NA12878_dragen_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@NA12878_dragen_vcf.snap new file mode 100644 index 00000000..83cde40d --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@NA12878_dragen_vcf.snap @@ -0,0 +1,183 @@ +--- +source: src/seqvars/ingest/mod.rs +expression: "std::fs::read_to_string(&args.path_out)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##SAMPLE= +##PEDIGREE= +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 +17 41244000 . T C . . gnomad_exomes_an=31346;gnomad_exomes_hom=1591;gnomad_exomes_het=6707;gnomad_genomes_an=250954;gnomad_genomes_hom=16402;gnomad_genomes_het=55703;clinvar_clinsig=benign;clinvar_rcv=RCV002490466;ANN=C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|10/23|c.3548A>G|p.K1183R|3661/7088|3548/5592|1183/1864|2878|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.3407A>G|p.K1136R|3601/7028|3407/5451|1136/1817|2878|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.788-951A>G|p.?|895/3696|788/2100||-950|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.3548A>G|p.K1183R|3661/7151|3548/5655|1183/1885|2878| GT:AD:DP:GQ 0/1:8:26:43 +17 41244435 . T C . . gnomad_exomes_an=31332;gnomad_exomes_hom=1505;gnomad_exomes_het=6415;gnomad_genomes_an=251032;gnomad_genomes_hom=16145;gnomad_genomes_het=55137;clinvar_clinsig=benign;clinvar_rcv=RCV001269365;ANN=C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|10/23|c.3113A>G|p.E1038G|3226/7088|3113/5592|1038/1864|2443|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2972A>G|p.E991G|3166/7028|2972/5451|991/1817|2443|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.788-1386A>G|p.?|895/3696|788/2100||-1385|,C|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.3113A>G|p.E1038G|3226/7151|3113/5655|1038/1885|2443| GT:AD:DP:GQ 0/1:12:26:47 +17 41244936 . G A . . gnomad_exomes_an=31324;gnomad_exomes_hom=4287;gnomad_exomes_het=6594;gnomad_genomes_an=251034;gnomad_genomes_hom=22738;gnomad_genomes_het=55898;clinvar_clinsig=benign;clinvar_rcv=RCV002496522;ANN=A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|10/23|c.2612C>T|p.P871L|2725/7088|2612/5592|871/1864|1942|,A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2471C>T|p.P824L|2665/7028|2471/5451|824/1817|1942|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1825C>T|p.?|894/3696|787/2100||1824|,A|missense_variant|MODERATE|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2612C>T|p.P871L|2725/7151|2612/5655|871/1885|1942| GT:AD:DP:GQ 0/1:17:30:47 +17 41245237 . A G . . gnomad_exomes_an=31314;gnomad_exomes_hom=1492;gnomad_exomes_het=6416;gnomad_genomes_an=250946;gnomad_genomes_hom=16057;gnomad_genomes_het=55063;clinvar_clinsig=benign;clinvar_rcv=RCV000755639;ANN=G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|10/23|c.2311T>C|p.L771=|2424/7088|2311/5592|771/1864|-1786|,G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.2170T>C|p.L724=|2364/7028|2170/5451|724/1817|-1786|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1524T>C|p.?|894/3696|787/2100||1523|,G|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2311T>C|p.L771=|2424/7151|2311/5655|771/1885|-1786| GT:AD:DP:GQ 0/1:18:29:46 +17 41245466 . G A . . gnomad_exomes_an=31338;gnomad_exomes_hom=1602;gnomad_exomes_het=6709;gnomad_genomes_an=251110;gnomad_genomes_hom=16420;gnomad_genomes_het=55707;clinvar_clinsig=benign;clinvar_rcv=RCV002477262;ANN=A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|10/23|c.2082C>T|p.S694=|2195/7088|2082/5592|694/1864|-2015|,A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|9/22|c.1941C>T|p.S647=|2135/7028|1941/5451|647/1817|-2015|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|10/21|c.787+1295C>T|p.?|894/3696|787/2100||1294|,A|synonymous_variant|LOW|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|10/24|c.2082C>T|p.S694=|2195/7151|2082/5655|694/1885|-2015| GT:AD:DP:GQ 0/1:11:19:48 +17 41247122 . A ACCT . . gnomad_exomes_an=31242;gnomad_exomes_hom=1750;gnomad_exomes_het=7017;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001709486;ANN=ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|9/22|c.671-246_671-245insAGG|p.?|784/7088|671/5592||-245|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|8/21|c.530-246_530-245insAGG|p.?|724/7028|530/5451||-245|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|9/21|c.671-246_671-245insAGG|p.?|778/3696|671/2100||-245|,ACCT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|9/23|c.671-246_671-245insAGG|p.?|784/7151|671/5655||-245| GT:AD:DP:GQ 0/1:18:29:45 +17 41247604 . A C . . gnomad_exomes_an=30832;gnomad_exomes_hom=1544;gnomad_exomes_het=6574;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001636715;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|9/22|c.670+259T>G|p.?|783/7088|670/5592||258|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|8/21|c.529+259T>G|p.?|723/7028|529/5451||258|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|9/21|c.670+259T>G|p.?|777/3696|670/2100||258|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|9/23|c.670+259T>G|p.?|783/7151|670/5655||258| GT:AD:DP:GQ 0/1:12:23:47 +17 41248164 . C T . . gnomad_exomes_an=31116;gnomad_exomes_hom=1468;gnomad_exomes_het=6372;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001668352;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/22|c.594-225G>A|p.?|707/7088|594/5592||-224|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-225G>A|p.?|647/7028|453/5451||-224|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-225G>A|p.?|701/3696|594/2100||-224|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-225G>A|p.?|707/7151|594/5655||-224| GT:AD:DP:GQ 0/1:14:21:44 +17 41248393 . C CAAAAAAAAAA . . ANN=CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/22|c.594-455_594-454insTTTTTTTTTT|p.?|707/7088|594/5592||-454|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-455_453-454insTTTTTTTTTT|p.?|647/7028|453/5451||-454|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-455_594-454insTTTTTTTTTT|p.?|701/3696|594/2100||-454|,CAAAAAAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-455_594-454insTTTTTTTTTT|p.?|707/7151|594/5655||-454| GT:AD:DP:GQ 0/1:9:16:48 +17 41248484 . G C . . gnomad_exomes_an=30426;gnomad_exomes_hom=1385;gnomad_exomes_het=6148;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001657973;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/22|c.594-545C>G|p.?|707/7088|594/5592||-544|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-545C>G|p.?|647/7028|453/5451||-544|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-545C>G|p.?|701/3696|594/2100||-544|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-545C>G|p.?|707/7151|594/5655||-544| GT:AD:DP:GQ 0/1:11:20:48 +17 41248588 . CA C . . gnomad_exomes_an=12806;gnomad_exomes_hom=585;gnomad_exomes_het=4704;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/22|c.594-650delT|p.?|707/7088|594/5592||-649|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.453-650delT|p.?|647/7028|453/5451||-649|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.594-650delT|p.?|701/3696|594/2100||-649|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.594-650delT|p.?|707/7151|594/5655||-649| GT:AD:DP:GQ 0/1:9:19:42 +17 41249094 . A G . . gnomad_exomes_an=31332;gnomad_exomes_hom=1602;gnomad_exomes_het=6703;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001610505;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|8/22|c.593+167T>C|p.?|706/7088|593/5592||166|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|7/21|c.452+167T>C|p.?|646/7028|452/5451||166|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|8/21|c.593+167T>C|p.?|700/3696|593/2100||166|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|8/23|c.593+167T>C|p.?|706/7151|593/5655||166| GT:AD:DP:GQ 0/1:9:16:48 +17 41249363 . TA T . . gnomad_exomes_an=31286;gnomad_exomes_hom=1497;gnomad_exomes_het=6409;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.548-58delT|p.?|661/7088|548/5592||-57|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.407-58delT|p.?|601/7028|407/5451||-57|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.548-58delT|p.?|655/3696|548/2100||-57|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.548-58delT|p.?|661/7151|548/5655||-57| GT:AD:DP:GQ 0/1:12:25:48 +17 41250047 . C CT . . gnomad_exomes_an=22188;gnomad_exomes_hom=992;gnomad_exomes_het=4281;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.548-742_548-741insA|p.?|661/7088|548/5592||-741|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.407-742_407-741insA|p.?|601/7028|407/5451||-741|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.548-742_548-741insA|p.?|655/3696|548/2100||-741|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.548-742_548-741insA|p.?|661/7151|548/5655||-741| GT:AD:DP:GQ 0/1:13:20:18 +17 41250678 . C CT . . gnomad_exomes_an=31058;gnomad_exomes_hom=1566;gnomad_exomes_het=6658;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191403;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.547+1113_547+1114insA|p.?|660/7088|547/5592||1113|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+1113_406+1114insA|p.?|600/7028|406/5451||1113|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+1113_547+1114insA|p.?|654/3696|547/2100||1113|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+1113_547+1114insA|p.?|660/7151|547/5655||1113| GT:AD:DP:GQ 0/1:6:22:42 +17 41250923 . T C . . gnomad_exomes_an=29782;gnomad_exomes_hom=4187;gnomad_exomes_het=6234;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191405;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.547+869A>G|p.?|660/7088|547/5592||868|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+869A>G|p.?|600/7028|406/5451||868|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+869A>G|p.?|654/3696|547/2100||868|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+869A>G|p.?|660/7151|547/5655||868| GT:AD:DP:GQ 0/1:13:22:47 +17 41251495 . C G . . gnomad_exomes_an=30850;gnomad_exomes_hom=1491;gnomad_exomes_het=6363;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001640278;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.547+297G>C|p.?|660/7088|547/5592||296|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+297G>C|p.?|600/7028|406/5451||296|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+297G>C|p.?|654/3696|547/2100||296|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+297G>C|p.?|660/7151|547/5655||296| GT:AD:DP:GQ 0/1:11:26:48 +17 41251646 . T A . . gnomad_exomes_an=31294;gnomad_exomes_hom=1592;gnomad_exomes_het=6693;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV002345409;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|7/22|c.547+146A>T|p.?|660/7088|547/5592||145|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|6/21|c.406+146A>T|p.?|600/7028|406/5451||145|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|7/21|c.547+146A>T|p.?|654/3696|547/2100||145|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|7/23|c.547+146A>T|p.?|660/7151|547/5655||145| GT:AD:DP:GQ 0/1:11:19:48 +17 41252575 . G A . . gnomad_exomes_an=6888;gnomad_exomes_hom=193;gnomad_exomes_het=1277;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191411;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-678C>T|p.?|555/7088|442/5592||-677|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-678C>T|p.?|495/7028|301/5451||-677|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-678C>T|p.?|549/3696|442/2100||-677|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-678C>T|p.?|555/7151|442/5655||-677| GT:AD:DP:GQ:PS 1|1:0:3:5:41252575 +17 41252591 . C CAT . . gnomad_exomes_an=10332;gnomad_exomes_hom=95;gnomad_exomes_het=571;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.442-695_442-694insAT|p.?|555/7088|442/5592||-694|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.301-695_301-694insAT|p.?|495/7028|301/5451||-694|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.442-695_442-694insAT|p.?|549/3696|442/2100||-694|,CAT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.442-695_442-694insAT|p.?|555/7151|442/5655||-694| GT:AD:DP:GQ:PS 1|1:0:2:4:41252575 +17 41254174 . A G . . gnomad_exomes_an=30142;gnomad_exomes_hom=1576;gnomad_exomes_het=6550;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191423;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1965T>C|p.?|554/7088|441/5592||1964|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1965T>C|p.?|494/7028|300/5451||1964|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1965T>C|p.?|548/3696|441/2100||1964|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1965T>C|p.?|554/7151|441/5655||1964| GT:AD:DP:GQ 0/1:14:27:48 +17 41254374 . C CTTTTTTTT . . gnomad_exomes_an=15994;gnomad_exomes_hom=494;gnomad_exomes_het=1743;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1764_441+1765insAAAAAAAA|p.?|554/7088|441/5592||1764|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1764_300+1765insAAAAAAAA|p.?|494/7028|300/5451||1764|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1764_441+1765insAAAAAAAA|p.?|548/3696|441/2100||1764|,CTTTTTTTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1764_441+1765insAAAAAAAA|p.?|554/7151|441/5655||1764| GT:AD:DP:GQ 0/1:6:13:48 +17 41254405 . C T . . gnomad_exomes_an=24316;gnomad_exomes_hom=1000;gnomad_exomes_het=4795;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000256092;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1734G>A|p.?|554/7088|441/5592||1733|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1734G>A|p.?|494/7028|300/5451||1733|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1734G>A|p.?|548/3696|441/2100||1733|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1734G>A|p.?|554/7151|441/5655||1733| GT:AD:DP:GQ 0/1:5:14:43 +17 41254486 . T G . . gnomad_exomes_an=30560;gnomad_exomes_hom=4284;gnomad_exomes_het=6345;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191424;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1653A>C|p.?|554/7088|441/5592||1652|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1653A>C|p.?|494/7028|300/5451||1652|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1653A>C|p.?|548/3696|441/2100||1652|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1653A>C|p.?|554/7151|441/5655||1652| GT:AD:DP:GQ 0/1:8:23:46 +17 41254965 . C CT . . gnomad_exomes_an=26726;gnomad_exomes_hom=2359;gnomad_exomes_het=6380;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255713;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1173_441+1174insA|p.?|554/7088|441/5592||1173|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1173_300+1174insA|p.?|494/7028|300/5451||1173|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1173_441+1174insA|p.?|548/3696|441/2100||1173|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1173_441+1174insA|p.?|554/7151|441/5655||1173| GT:AD:DP:GQ 0/1:14:22:22 +17 41255102 . A G . . gnomad_exomes_an=31104;gnomad_exomes_hom=1426;gnomad_exomes_het=6400;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191428;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1037T>C|p.?|554/7088|441/5592||1036|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1037T>C|p.?|494/7028|300/5451||1036|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1037T>C|p.?|548/3696|441/2100||1036|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1037T>C|p.?|554/7151|441/5655||1036| GT:AD:DP:GQ:PS 0|1:19:31:46:41255102 +17 41255111 . A T . . gnomad_exomes_an=31114;gnomad_exomes_hom=1530;gnomad_exomes_het=6684;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191429;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+1028T>A|p.?|554/7088|441/5592||1027|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+1028T>A|p.?|494/7028|300/5451||1027|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+1028T>A|p.?|548/3696|441/2100||1027|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+1028T>A|p.?|554/7151|441/5655||1027| GT:AD:DP:GQ:PS 0|1:19:31:46:41255102 +17 41256074 . CA C . . gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+64delT|p.?|554/7088|441/5592||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||63| GT:AD:DP:GQ:PS 0|1:11:17:43:41256074 +17 41256089 . AAAAAAAAAGAAAAG A . . gnomad_exomes_an=28388;gnomad_exomes_hom=1079;gnomad_exomes_het=5744;gnomad_genomes_an=167932;gnomad_genomes_hom=9911;gnomad_genomes_het=23697;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|554/7088|441/5592||35|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+36_300+49delCTTTTCTTTTTTTT|p.?|494/7028|300/5451||35|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|548/3696|441/2100||35|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+36_441+49delCTTTTCTTTTTTTT|p.?|554/7151|441/5655||35| GT:AD:DP:GQ:PS 0|1:13:19:43:41256074 +17 41257134 . T C . . gnomad_exomes_an=31346;gnomad_exomes_hom=4418;gnomad_exomes_het=6505;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV002415590;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|4/22|c.213-161A>G|p.?|326/7088|213/5592||-160|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.72-161A>G|p.?|266/7028|72/5451||-160|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.213-161A>G|p.?|320/3696|213/2100||-160|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.213-161A>G|p.?|326/7151|213/5655||-160| GT:AD:DP:GQ 0/1:14:29:48 +17 41257458 . A C . . gnomad_exomes_an=31258;gnomad_exomes_hom=1500;gnomad_exomes_het=6414;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191434;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|4/22|c.213-485T>G|p.?|326/7088|213/5592||-484|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.72-485T>G|p.?|266/7028|72/5451||-484|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.213-485T>G|p.?|320/3696|213/2100||-484|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.213-485T>G|p.?|326/7151|213/5655||-484| GT:AD:DP:GQ 0/1:11:26:48 +17 41258043 . C T . . gnomad_exomes_an=30426;gnomad_exomes_hom=1538;gnomad_exomes_het=6460;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191436;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|4/22|c.212+430G>A|p.?|325/7088|212/5592||429|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.71+430G>A|p.?|265/7028|71/5451||429|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.212+430G>A|p.?|319/3696|212/2100||429|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.212+430G>A|p.?|325/7151|212/5655||429| GT:AD:DP:GQ 0/1:14:27:48 +17 41258135 . T TA . . gnomad_exomes_an=20132;gnomad_exomes_hom=1;gnomad_exomes_het=267;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|4/22|c.212+337_212+338insT|p.?|325/7088|212/5592||337|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|3/21|c.71+337_71+338insT|p.?|265/7028|71/5451||337|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|4/21|c.212+337_212+338insT|p.?|319/3696|212/2100||337|,TA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|4/23|c.212+337_212+338insT|p.?|325/7151|212/5655||337| GT:AD:DP:GQ 1/1:3:14:4 +17 41259049 . C T . . gnomad_exomes_an=30790;gnomad_exomes_hom=1585;gnomad_exomes_het=6633;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191440;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-499G>A|p.?|248/7088|135/5592||-498|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-499G>A|p.?|188/7028|-7/5451||-498|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-499G>A|p.?|242/3696|135/2100||-498|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-499G>A|p.?|248/7151|135/5655||-498| GT:AD:DP:GQ 0/1:8:16:48 +17 41259079 . A ATT . . gnomad_exomes_an=21472;gnomad_exomes_hom=898;gnomad_exomes_het=3635;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-530_135-529insAA|p.?|248/7088|135/5592||-529|,ATT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-530_-7-529insAA|p.?|188/7028|-7/5451||-529|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-530_135-529insAA|p.?|242/3696|135/2100||-529|,ATT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-530_135-529insAA|p.?|248/7151|135/5655||-529| GT:AD:DP:GQ 0/1:10:13:7 +17 41259113 . G A . . gnomad_exomes_an=26218;gnomad_exomes_hom=2;gnomad_exomes_het=204;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255936;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-563C>T|p.?|248/7088|135/5592||-562|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-563C>T|p.?|188/7028|-7/5451||-562|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-563C>T|p.?|242/3696|135/2100||-562|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-563C>T|p.?|248/7151|135/5655||-562| GT:AD:DP:GQ 0/1:11:19:48 +17 41260352 . C CA . . gnomad_exomes_an=19754;gnomad_exomes_hom=856;gnomad_exomes_het=4728;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255985;ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-1803_135-1802insT|p.?|248/7088|135/5592||-1802|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-1803_-7-1802insT|p.?|188/7028|-7/5451||-1802|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-1803_135-1802insT|p.?|242/3696|135/2100||-1802|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-1803_135-1802insT|p.?|248/7151|135/5655||-1802| GT:AD:DP:GQ 0/1:11:19:43 +17 41260723 . C CAAAAA . . ANN=CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-2174_135-2173insTTTTT|p.?|248/7088|135/5592||-2173|,CAAAAA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2174_-7-2173insTTTTT|p.?|188/7028|-7/5451||-2173|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2174_135-2173insTTTTT|p.?|242/3696|135/2100||-2173|,CAAAAA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2174_135-2173insTTTTT|p.?|248/7151|135/5655||-2173| GT:AD:DP:GQ 0/1:1:2:20 +17 41260808 . A G . . gnomad_exomes_an=30782;gnomad_exomes_hom=1558;gnomad_exomes_het=6565;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191445;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-2258T>C|p.?|248/7088|135/5592||-2257|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2258T>C|p.?|188/7028|-7/5451||-2257|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2258T>C|p.?|242/3696|135/2100||-2257|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2258T>C|p.?|248/7151|135/5655||-2257| GT:AD:DP:GQ 0/1:12:15:32 +17 41261058 . T TCTATCTATCTACCTAC . . gnomad_exomes_an=31232;gnomad_exomes_hom=1461;gnomad_exomes_het=6772;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255302;ANN=TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|248/7088|135/5592||-2508|,TCTATCTATCTACCTAC|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2509_-7-2508insGTAGGTAGATAGATAG|p.?|188/7028|-7/5451||-2508|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|242/3696|135/2100||-2508|,TCTATCTATCTACCTAC|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2509_135-2508insGTAGGTAGATAGATAG|p.?|248/7151|135/5655||-2508| GT:AD:DP:GQ 0/1:9:20:48 +17 41261233 . C T . . gnomad_exomes_an=31268;gnomad_exomes_hom=1604;gnomad_exomes_het=6702;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191449;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-2683G>A|p.?|248/7088|135/5592||-2682|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-2683G>A|p.?|188/7028|-7/5451||-2682|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-2683G>A|p.?|242/3696|135/2100||-2682|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-2683G>A|p.?|248/7151|135/5655||-2682| GT:AD:DP:GQ 0/1:12:27:48 +17 41263044 . A G . . gnomad_exomes_an=30560;gnomad_exomes_hom=1541;gnomad_exomes_het=6552;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191458;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-4494T>C|p.?|248/7088|135/5592||-4493|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-4494T>C|p.?|188/7028|-7/5451||-4493|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-4494T>C|p.?|242/3696|135/2100||-4493|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-4494T>C|p.?|248/7151|135/5655||-4493| GT:AD:DP:GQ 0/1:7:14:48 +17 41263117 . C CA . . gnomad_exomes_an=17480;gnomad_exomes_hom=629;gnomad_exomes_het=3959;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.135-4568_135-4567insT|p.?|248/7088|135/5592||-4567|,CA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-4568_-7-4567insT|p.?|188/7028|-7/5451||-4567|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.135-4568_135-4567insT|p.?|242/3696|135/2100||-4567|,CA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.135-4568_135-4567insT|p.?|248/7151|135/5655||-4567| GT:AD:DP:GQ 0/1:13:23:34 +17 41263566 . T C . . gnomad_exomes_an=29818;gnomad_exomes_hom=1603;gnomad_exomes_het=6680;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191462;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+4177A>G|p.?|247/7088|134/5592||4176|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5016A>G|p.?|188/7028|-7/5451||-5015|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+4177A>G|p.?|241/3696|134/2100||4176|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+4177A>G|p.?|247/7151|134/5655||4176| GT:AD:DP:GQ 0/1:11:19:48 +17 41264146 . G A . . gnomad_exomes_an=30782;gnomad_exomes_hom=1483;gnomad_exomes_het=6307;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191465;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+3597C>T|p.?|247/7088|134/5592||3596|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5596C>T|p.?|188/7028|-7/5451||-5595|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3597C>T|p.?|241/3696|134/2100||3596|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3597C>T|p.?|247/7151|134/5655||3596| GT:AD:DP:GQ 0/1:13:20:45 +17 41264364 . A G . . gnomad_exomes_an=31320;gnomad_exomes_hom=1500;gnomad_exomes_het=6409;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191467;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+3379T>C|p.?|247/7088|134/5592||3378|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-5814T>C|p.?|188/7028|-7/5451||-5813|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3379T>C|p.?|241/3696|134/2100||3378|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3379T>C|p.?|247/7151|134/5655||3378| GT:AD:DP:GQ 0/1:8:24:45 +17 41264739 . C T . . gnomad_exomes_an=30908;gnomad_exomes_hom=3162;gnomad_exomes_het=7226;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255084;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+3004G>A|p.?|247/7088|134/5592||3003|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6189G>A|p.?|188/7028|-7/5451||-6188|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3004G>A|p.?|241/3696|134/2100||3003|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3004G>A|p.?|247/7151|134/5655||3003| GT:AD:DP:GQ:PS 0|1:14:29:48:41264739 +17 41264740 . TGA T . . gnomad_exomes_an=31014;gnomad_exomes_hom=3159;gnomad_exomes_het=7229;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+3001_134+3002delTC|p.?|247/7088|134/5592||3000|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6192_-7-6191delTC|p.?|188/7028|-7/5451||-6190|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+3001_134+3002delTC|p.?|241/3696|134/2100||3000|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+3001_134+3002delTC|p.?|247/7151|134/5655||3000| GT:AD:DP:GQ 0/1:14:30:48 +17 41264743 . CT C . . gnomad_exomes_an=30890;gnomad_exomes_hom=3155;gnomad_exomes_het=7228;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2999delA|p.?|247/7088|134/5592||2998|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6194delA|p.?|188/7028|-7/5451||-6193|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2999delA|p.?|241/3696|134/2100||2998|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2999delA|p.?|247/7151|134/5655||2998| GT:AD:DP:GQ:PS 0|1:14:29:48:41264739 +17 41264749 . C G . . gnomad_exomes_an=30892;gnomad_exomes_hom=3135;gnomad_exomes_het=7223;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000256095;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2994G>C|p.?|247/7088|134/5592||2993|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6199G>C|p.?|188/7028|-7/5451||-6198|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2994G>C|p.?|241/3696|134/2100||2993|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2994G>C|p.?|247/7151|134/5655||2993| GT:AD:DP:GQ:PS 0|1:14:29:48:41264739 +17 41264750 . A T . . gnomad_exomes_an=30880;gnomad_exomes_hom=3136;gnomad_exomes_het=7219;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255162;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2993T>A|p.?|247/7088|134/5592||2992|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6200T>A|p.?|188/7028|-7/5451||-6199|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2993T>A|p.?|241/3696|134/2100||2992|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2993T>A|p.?|247/7151|134/5655||2992| GT:AD:DP:GQ:PS 0|1:14:29:48:41264739 +17 41264751 . A AGGG . . gnomad_exomes_an=30776;gnomad_exomes_hom=3136;gnomad_exomes_het=7222;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2991_134+2992insCCC|p.?|247/7088|134/5592||2991|,AGGG|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6202_-7-6201insCCC|p.?|188/7028|-7/5451||-6201|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2991_134+2992insCCC|p.?|241/3696|134/2100||2991|,AGGG|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2991_134+2992insCCC|p.?|247/7151|134/5655||2991| GT:AD:DP:GQ:PS 0|1:14:29:48:41264739 +17 41264753 . C T . . gnomad_exomes_an=30714;gnomad_exomes_hom=3130;gnomad_exomes_het=7189;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255582;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2990G>A|p.?|247/7088|134/5592||2989|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6203G>A|p.?|188/7028|-7/5451||-6202|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2990G>A|p.?|241/3696|134/2100||2989|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2990G>A|p.?|247/7151|134/5655||2989| GT:AD:DP:GQ:PS 0|1:14:27:48:41264739 +17 41264755 . TGAAAC T . . gnomad_exomes_an=30768;gnomad_exomes_hom=3130;gnomad_exomes_het=7187;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+2983_134+2987delGTTTC|p.?|247/7088|134/5592||2982|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-6210_-7-6206delGTTTC|p.?|188/7028|-7/5451||-6205|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+2983_134+2987delGTTTC|p.?|241/3696|134/2100||2982|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+2983_134+2987delGTTTC|p.?|247/7151|134/5655||2982| GT:AD:DP:GQ:PS 0|1:14:27:48:41264739 +17 41265776 . A G . . gnomad_exomes_an=31332;gnomad_exomes_hom=1615;gnomad_exomes_het=6700;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191470;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+1967T>C|p.?|247/7088|134/5592||1966|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-7226T>C|p.?|188/7028|-7/5451||-7225|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+1967T>C|p.?|241/3696|134/2100||1966|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+1967T>C|p.?|247/7151|134/5655||1966| GT:AD:DP:GQ 0/1:23:37:44 +17 41266407 . C CT . . gnomad_exomes_an=22904;gnomad_exomes_hom=2326;gnomad_exomes_het=5197;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255595;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+1335_134+1336insA|p.?|247/7088|134/5592||1335|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-7858_-7-7857insA|p.?|188/7028|-7/5451||-7857|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+1335_134+1336insA|p.?|241/3696|134/2100||1335|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+1335_134+1336insA|p.?|247/7151|134/5655||1335| GT:AD:DP:GQ 0/1:10:18:33 +17 41267050 . G A . . gnomad_exomes_an=31332;gnomad_exomes_hom=1619;gnomad_exomes_het=6726;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191477;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+693C>T|p.?|247/7088|134/5592||692|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-7-8500C>T|p.?|188/7028|-7/5451||-8499|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+693C>T|p.?|241/3696|134/2100||692|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+693C>T|p.?|247/7151|134/5655||692| GT:AD:DP:GQ 0/1:7:23:44 +17 41267518 . CA C . . gnomad_exomes_an=21564;gnomad_exomes_hom=937;gnomad_exomes_het=6113;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|3/22|c.134+224delT|p.?|247/7088|134/5592||223|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+8515delT|p.?|187/7028|-8/5451||8514|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|3/21|c.134+224delT|p.?|241/3696|134/2100||223|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|3/23|c.134+224delT|p.?|247/7151|134/5655||223| GT:AD:DP:GQ 0/1:11:19:35 +17 41268206 . A C . . gnomad_exomes_an=31210;gnomad_exomes_hom=1544;gnomad_exomes_het=6707;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191483;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-410T>G|p.?|194/7088|81/5592||-409|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+7828T>G|p.?|187/7028|-8/5451||7827|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-410T>G|p.?|188/3696|81/2100||-409|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-410T>G|p.?|194/7151|81/5655||-409| GT:AD:DP:GQ:PS 0|1:13:22:46:41268206 +17 41268208 . C CT . . gnomad_exomes_an=31128;gnomad_exomes_hom=1385;gnomad_exomes_het=6554;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000255730;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-413_81-412insA|p.?|194/7088|81/5592||-412|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+7825_-8+7826insA|p.?|187/7028|-8/5451||7825|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-413_81-412insA|p.?|188/3696|81/2100||-412|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-413_81-412insA|p.?|194/7151|81/5655||-412| GT:AD:DP:GQ:PS 0|1:13:22:46:41268206 +17 41270229 . T G . . gnomad_exomes_an=31274;gnomad_exomes_hom=1606;gnomad_exomes_het=6696;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191491;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-2433A>C|p.?|194/7088|81/5592||-2432|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5805A>C|p.?|187/7028|-8/5451||5804|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2433A>C|p.?|188/3696|81/2100||-2432|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2433A>C|p.?|194/7151|81/5655||-2432| GT:AD:DP:GQ 0/1:7:24:40 +17 41270277 . C T . . gnomad_exomes_an=31338;gnomad_exomes_hom=1513;gnomad_exomes_het=6416;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191493;ANN=T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-2481G>A|p.?|194/7088|81/5592||-2480|,T|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5757G>A|p.?|187/7028|-8/5451||5756|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2481G>A|p.?|188/3696|81/2100||-2480|,T|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2481G>A|p.?|194/7151|81/5655||-2480| GT:AD:DP:GQ 0/1:9:22:48 +17 41270463 . G A . . gnomad_exomes_an=30876;gnomad_exomes_hom=1578;gnomad_exomes_het=6604;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191497;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-2667C>T|p.?|194/7088|81/5592||-2666|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5571C>T|p.?|187/7028|-8/5451||5570|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2667C>T|p.?|188/3696|81/2100||-2666|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2667C>T|p.?|194/7151|81/5655||-2666| GT:AD:DP:GQ 0/1:15:28:48 +17 41270666 . C A . . gnomad_exomes_an=31306;gnomad_exomes_hom=1500;gnomad_exomes_het=6413;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191498;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-2870G>T|p.?|194/7088|81/5592||-2869|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5368G>T|p.?|187/7028|-8/5451||5367|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2870G>T|p.?|188/3696|81/2100||-2869|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2870G>T|p.?|194/7151|81/5655||-2869| GT:AD:DP:GQ 0/1:11:15:43 +17 41270778 . C CT . . gnomad_exomes_an=23434;gnomad_exomes_hom=923;gnomad_exomes_het=4562;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000256051;ANN=CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-2983_81-2982insA|p.?|194/7088|81/5592||-2982|,CT|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+5255_-8+5256insA|p.?|187/7028|-8/5451||5255|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-2983_81-2982insA|p.?|188/3696|81/2100||-2982|,CT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-2983_81-2982insA|p.?|194/7151|81/5655||-2982| GT:AD:DP:GQ 0/1:11:16:14 +17 41271293 . GA G . . gnomad_exomes_an=26204;gnomad_exomes_hom=4218;gnomad_exomes_het=6049;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.81-3498delT|p.?|194/7088|81/5592||-3497|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+4740delT|p.?|187/7028|-8/5451||4739|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.81-3498delT|p.?|188/3696|81/2100||-3497|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.81-3498delT|p.?|194/7151|81/5655||-3497| GT:AD:DP:GQ 0/1:10:20:48 +17 41273095 . G A . . gnomad_exomes_an=27498;gnomad_exomes_hom=1472;gnomad_exomes_het=6401;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191505;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2939C>T|p.?|193/7088|80/5592||2938|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2939C>T|p.?|187/7028|-8/5451||2938|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2939C>T|p.?|187/3696|80/2100||2938|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2939C>T|p.?|193/7151|80/5655||2938| GT:AD:DP:GQ 0/1:12:20:47 +17 41273348 . T C . . gnomad_exomes_an=31018;gnomad_exomes_hom=4264;gnomad_exomes_het=6559;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191507;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2686A>G|p.?|193/7088|80/5592||2685|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2686A>G|p.?|187/7028|-8/5451||2685|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2686A>G|p.?|187/3696|80/2100||2685|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2686A>G|p.?|193/7151|80/5655||2685| GT:AD:DP:GQ 0/1:18:31:47 +17 41273379 . G C . . gnomad_exomes_an=30948;gnomad_exomes_hom=1487;gnomad_exomes_het=6371;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191508;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2655C>G|p.?|193/7088|80/5592||2654|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2655C>G|p.?|187/7028|-8/5451||2654|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2655C>G|p.?|187/3696|80/2100||2654|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2655C>G|p.?|193/7151|80/5655||2654| GT:AD:DP:GQ 0/1:19:33:47 +17 41273537 . A C . . gnomad_exomes_an=30662;gnomad_exomes_hom=1552;gnomad_exomes_het=6479;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191510;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+2497T>G|p.?|193/7088|80/5592||2496|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+2497T>G|p.?|187/7028|-8/5451||2496|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+2497T>G|p.?|187/3696|80/2100||2496|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+2497T>G|p.?|193/7151|80/5655||2496| GT:AD:DP:GQ 0/1:14:33:48 +17 41274778 . G A . . gnomad_exomes_an=31152;gnomad_exomes_hom=1594;gnomad_exomes_het=6661;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191511;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+1256C>T|p.?|193/7088|80/5592||1255|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+1256C>T|p.?|187/7028|-8/5451||1255|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+1256C>T|p.?|187/3696|80/2100||1255|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+1256C>T|p.?|193/7151|80/5655||1255| GT:AD:DP:GQ 0/1:11:27:48 +17 41274906 . G A . . gnomad_exomes_an=28872;gnomad_exomes_hom=3662;gnomad_exomes_het=6225;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191514;ANN=A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+1128C>T|p.?|193/7088|80/5592||1127|,A|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+1128C>T|p.?|187/7028|-8/5451||1127|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+1128C>T|p.?|187/3696|80/2100||1127|,A|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+1128C>T|p.?|193/7151|80/5655||1127| GT:AD:DP:GQ 0/1:17:27:47 +17 41275081 . G GA . . gnomad_exomes_an=29534;gnomad_exomes_hom=1365;gnomad_exomes_het=6118;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191515;ANN=GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+952_80+953insT|p.?|193/7088|80/5592||952|,GA|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+952_-8+953insT|p.?|187/7028|-8/5451||952|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+952_80+953insT|p.?|187/3696|80/2100||952|,GA|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+952_80+953insT|p.?|193/7151|80/5655||952| GT:AD:DP:GQ 0/1:10:22:47 +17 41275151 . G C . . gnomad_exomes_an=31080;gnomad_exomes_hom=1493;gnomad_exomes_het=6342;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV000191516;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+883C>G|p.?|193/7088|80/5592||882|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+883C>G|p.?|187/7028|-8/5451||882|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+883C>G|p.?|187/3696|80/2100||882|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+883C>G|p.?|193/7151|80/5655||882| GT:AD:DP:GQ 0/1:15:28:48 +17 41275366 . GTTTTTTT G . . ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+661_80+667delAAAAAAA|p.?|193/7088|80/5592||660|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+661_-8+667delAAAAAAA|p.?|187/7028|-8/5451||660|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+661_80+667delAAAAAAA|p.?|187/3696|80/2100||660|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+661_80+667delAAAAAAA|p.?|193/7151|80/5655||660| GT:AD:DP:GQ 0/1:10:21:48 +17 41275645 . A G . . gnomad_exomes_an=31292;gnomad_exomes_hom=1615;gnomad_exomes_het=6682;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001689724;ANN=G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|2/22|c.80+389T>C|p.?|193/7088|80/5592||388|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|2/21|c.-8+389T>C|p.?|187/7028|-8/5451||388|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|2/21|c.80+389T>C|p.?|187/3696|80/2100||388|,G|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|2/23|c.80+389T>C|p.?|193/7151|80/5655||388| GT:AD:DP:GQ 0/1:15:32:48 +17 41276247 . A G . . gnomad_exomes_an=31318;gnomad_exomes_hom=1611;gnomad_exomes_het=6702;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001610389;ANN=G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|1/22|c.-19-115T>C|p.?|95/7088|-19/5592||-114|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-106-115T>C|p.?|89/7028|-106/5451||-114|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-19-115T>C|p.?|89/3696|-19/2100||-114|,G|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-19-115T>C|p.?|95/7151|-19/5655||-114| GT:AD:DP:GQ 0/1:18:28:44 +17 41276348 . T C . . gnomad_exomes_an=31332;gnomad_exomes_hom=1609;gnomad_exomes_het=6706;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;clinvar_clinsig=benign;clinvar_rcv=RCV001711604;ANN=C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|1/22|c.-19-216A>G|p.?|95/7088|-19/5592||-215|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-106-216A>G|p.?|89/7028|-106/5451||-215|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-19-216A>G|p.?|89/3696|-19/2100||-215|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-19-216A>G|p.?|95/7151|-19/5655||-215| GT:AD:DP:GQ 0/1:17:30:47 +17 41277187 . G C . . gnomad_exomes_an=29432;gnomad_exomes_hom=4088;gnomad_exomes_het=6345;gnomad_genomes_an=128296;gnomad_genomes_hom=11705;gnomad_genomes_het=29182;clinvar_clinsig=benign;clinvar_rcv=RCV001711453;ANN=C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|1/22|c.-20+101C>G|p.?|94/7088|-20/5592||100|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|1/21|c.-107+107C>G|p.?|88/7028|-107/5451||106|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|1/21|c.-20+107C>G|p.?|88/3696|-20/2100||106|,C|5_prime_UTR_variant&intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|1/23|c.-20+101C>G|p.?|94/7151|-20/5655||100| GT:AD:DP:GQ 0/1:14:28:48 +MT 152 . T C . . . GT:GQ:AD:DP 1/1:98.13:2:10584 +MT 263 . A G . . . GT:GQ:AD:DP 1/1:98.13:0:7628 +MT 302 . A AC . . . GT:GQ:AD:DP 1/1:96.52:40:3536 +MT 310 . T TC . . . GT:GQ:AD:DP 1/1:96.88:7:3742 +MT 310 . T C . . . GT:GQ:AD:DP 0/1:21.54:7:3742 +MT 539 . T A . . . GT:GQ:AD:DP 0/1:21.53:6115:6405 +MT 596 . T A . . . GT:GQ:AD:DP 0/1:17.66:7690:7850 +MT 605 . T A . . . GT:GQ:AD:DP 0/1:21.53:5916:6058 +MT 610 . T A . . . GT:GQ:AD:DP 0/1:3.4:5986:6129 +MT 616 . T A . . . GT:GQ:AD:DP 0/1:0.12:6178:6261 +MT 750 . A G . . . GT:GQ:AD:DP 1/1:98.13:1:7819 +MT 1438 . A G . . . GT:GQ:AD:DP 1/1:98.13:2:9170 +MT 2141 . T TAG . . . GT:GQ:AD:DP 0/1:20:6260:6286 +MT 2259 . C T . . . GT:GQ:AD:DP 1/1:98.13:3:7528 +MT 2645 . G A . . . GT:GQ:AD:DP 0/1:21.53:9159:9193 +MT 3572 . T G . . . GT:GQ:AD:DP 0/1:21.53:6937:7895 +MT 3572 . T A . . . GT:GQ:AD:DP 0/1:21.49:6937:7895 +MT 3577 . A C . . . GT:GQ:AD:DP 0/1:21.53:7519:7979 +MT 3578 . T A . . . GT:GQ:AD:DP 0/1:21.53:7041:7921 +MT 3578 . T G . . . GT:GQ:AD:DP 0/1:21.53:7041:7921 +MT 3583 . A C . . . GT:GQ:AD:DP 0/1:21.53:7746:8049 +MT 3590 . T A . . . GT:GQ:AD:DP 0/1:21.53:6859:7638 +MT 3593 . T G . . . GT:GQ:AD:DP 0/1:0.51:7844:8078 +MT 3595 . A C . . . GT:GQ:AD:DP 0/1:21.22:7958:8111 +MT 3599 . T A . . . GT:GQ:AD:DP 0/1:21.53:7408:7913 +MT 3605 . T A . . . GT:GQ:AD:DP 0/1:21.53:5371:5645 +MT 3614 . T A . . . GT:GQ:AD:DP 0/1:20.35:5553:5689 +MT 3631 . T A . . . GT:GQ:AD:DP 0/1:20.17:5740:5893 +MT 3633 . T A . . . GT:GQ:AD:DP 0/1:10.82:5829:5943 +MT 4434 . T G . . . GT:GQ:AD:DP 0/1:0.79:7711:7878 +MT 4491 . G A . . . GT:GQ:AD:DP 0/1:14.25:6096:6108 +MT 4745 . A G . . . GT:GQ:AD:DP:PS 1|1:94.1:0:4255:4745 +MT 4769 . A G . . . GT:GQ:AD:DP:PS 1|1:96.49:0:4115:4745 +MT 6518 . C T . . . GT:GQ:AD:DP 0/1:21.4:9464:9504 +MT 7337 . G A . . . GT:GQ:AD:DP 1/1:93.49:2:8855 +MT 8129 . A C . . . GT:GQ:AD:DP 0/1:20.26:7971:8173 +MT 8860 . A G . . . GT:GQ:AD:DP 1/1:91.87:0:4988 +MT 13326 . T C . . . GT:GQ:AD:DP 1/1:98.13:2:9163 +MT 13680 . C T . . . GT:GQ:AD:DP 1/1:98.13:1:5581 +MT 13680 . C G . . . GT:GQ:AD:DP 0/1:25.75:1:5581 +MT 13752 . T G . . . GT:GQ:AD:DP 0/1:21.51:4714:4779 +MT 13762 . T G . . . GT:GQ:AD:DP 0/1:21.53:4509:4689 +MT 13768 . T G . . . GT:GQ:AD:DP 0/1:21.53:4623:4778 +MT 13769 . T G . . . GT:GQ:AD:DP 0/1:21.53:4684:4799 +MT 14831 . G A . . . GT:GQ:AD:DP 1/1:98.13:3:8846 +MT 14831 . G C . . . GT:GQ:AD:DP 0/1:49.84:3:8846 +MT 14872 . C T . . . GT:GQ:AD:DP 1/1:98.13:5:6667 +MT 14918 . G A . . . GT:GQ:AD:DP 0/1:21.37:6570:6807 +MT 15326 . A G . . . GT:GQ:AD:DP 1/1:98.13:1:7648 +MT 16023 . G A . . . GT:GQ:AD:DP 0/1:51.92:2572:9277 + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_4_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_4_vcf.snap new file mode 100644 index 00000000..e86161e4 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_4_vcf.snap @@ -0,0 +1,56 @@ +--- +source: src/seqvars/ingest/mod.rs +expression: "std::fs::read_to_string(&args.path_out)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##SAMPLE= +##PEDIGREE= +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 +17 41256074 . CA C . . gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+64delT|p.?|554/7088|441/5592||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||63| GT:AD:DP:GQ:PS 0|1:11:17:43:41256074 +MT 750 . A G . . . GT:GQ:AD:DP 1/1:98.13:1:7819 + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_9_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_9_vcf.snap new file mode 100644 index 00000000..b8c53f53 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_dragen_07_021_624_3_10_9_vcf.snap @@ -0,0 +1,56 @@ +--- +source: src/seqvars/ingest/mod.rs +expression: "std::fs::read_to_string(&args.path_out)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##SAMPLE= +##PEDIGREE= +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CASE +17 41256074 . CA C . . gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+64delT|p.?|554/7088|441/5592||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||63| GT:AD:DP:GQ:PS 0|1:18:32:47:41256074 +MT 750 . A G . . . GT:GQ:AD:DP 1/1:98.13:1:5608 + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_3_7-0_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_3_7-0_vcf.snap new file mode 100644 index 00000000..3399500d --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_3_7-0_vcf.snap @@ -0,0 +1,60 @@ +--- +source: src/seqvars/ingest/mod.rs +expression: "std::fs::read_to_string(&args.path_out)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##SAMPLE= +##SAMPLE= +##SAMPLE= +##PEDIGREE= +##PEDIGREE= +##PEDIGREE= +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Case_1_father-N1-DNA1-WGS1 Case_1_index-N1-DNA1-WGS1 Case_1_mother-N1-DNA1-WGS1 +17 41210126 . C CTAGCACTT . . gnomad_exomes_an=31272;gnomad_exomes_hom=0;gnomad_exomes_het=85;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|18/22|c.5194-975_5194-974insAAGTGCTA|p.?|5307/7088|5194/5592||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|17/21|c.5053-975_5053-974insAAGTGCTA|p.?|5247/7028|5053/5451||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|18/21|c.1882-975_1882-974insAAGTGCTA|p.?|1989/3696|1882/2100||-974|,CTAGCACTT|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|19/23|c.5257-975_5257-974insAAGTGCTA|p.?|5370/7151|5257/5655||-974| GT:AD:DP:GQ 0/0:29:29:87 0/1:23:36:99 0/1:15:32:99 +MT 750 . A G . . . GT:AD:DP:GQ 1/1:0:2757:99 1/1:0:2392:99 1/1:0:1621:99 + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_4_4_0_0_vcf.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_4_4_0_0_vcf.snap new file mode 100644 index 00000000..0a627942 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test@example_gatk_hc_4_4_0_0_vcf.snap @@ -0,0 +1,56 @@ +--- +source: src/seqvars/ingest/mod.rs +expression: "std::fs::read_to_string(&args.path_out)?" +--- +##fileformat=VCFv4.4 +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FILTER= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##SAMPLE= +##PEDIGREE= +##x-varfish-version= +##x-varfish-version= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CASE +17 41256074 . CA C . . gnomad_exomes_an=20150;gnomad_exomes_hom=2725;gnomad_exomes_het=5476;gnomad_genomes_an=0;gnomad_genomes_hom=0;gnomad_genomes_het=0;ANN=C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007294.4|Coding|6/22|c.441+64delT|p.?|554/7088|441/5592||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007297.4|Coding|5/21|c.300+64delT|p.?|494/7028|300/5451||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007299.4|Coding|6/21|c.441+64delT|p.?|548/3696|441/2100||63|,C|intron_variant|MODIFIER|BRCA1|HGNC:1100|transcript|NM_007300.4|Coding|6/23|c.441+64delT|p.?|554/7151|441/5655||63| GT:AD:DP:GQ:PS 1|1:0:80:99:41256074 +MT 750 . A G . . . GT:AD:DP:GQ 1/1:0:35:99 + diff --git a/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_gz.snap b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_gz.snap new file mode 100644 index 00000000..5fa7e8b1 --- /dev/null +++ b/src/seqvars/ingest/snapshots/varfish_server_worker__seqvars__ingest__test__result_snapshot_test_gz.snap @@ -0,0 +1,514 @@ +--- +source: src/seqvars/ingest/mod.rs +expression: "String::from_utf8_lossy(&buffer)" +--- +0000: 1F 8B 08 00 00 00 00 00 00 FF CD 9D 59 73 1B 47 ............Ys.G +0016: 92 80 9F 39 BF 82 21 47 EC 3C 48 84 EA 3E A0 A5 ...9..!G... +0032: 36 30 A4 0C 2B D6 92 35 14 C6 B3 FB 84 A0 69 58 60..+..5......iX +0048: 62 8C 48 6A 49 DA 6B 6F E0 C7 6F D6 D5 E8 23 AB b.HjI.ko..o...#. +0064: 41 B2 AB 3B AC 19 A9 61 F4 91 59 59 5F 25 B2 B2 A..;...a..YY_%.. +0080: 8E FE E6 9B 5F 2E BF 6C 7E B9 B9 BD 3A BF 3F FE ...._..l~...:.?. +0096: F1 E4 DB DF C4 4C FC E5 9B 6F DE BE FF F6 87 E3 .....L...o...... +0112: 7F 7F 7B 7A FC E9 FA E6 EA FC E7 F5 E6 F7 9B AB ..{z............ +0128: CD DD FA FC FA C5 FB 5F AF 7E DA DC 1E D3 17 AB ......._.~...... +0144: 3F BE 6E 8E DF 5E DF 6F 3E 6D 6E 5F 9C 6E EE 2E ?.n..^.o>mn_.n.. +0160: 6E 2F BF DE 5F DE 5C 1F 3F 0B 97 1C DE FC 72 78 n/.._.\.?.....rx +0176: 77 7E F5 F5 CB E6 EE F0 F2 FA D0 3D 68 71 7A 18 w~.........=hqz. +0192: 1E F4 EC 75 5E C6 E7 9B AB C7 09 81 1B 66 87 E7 ...u^........f.. +0208: 5F EE 67 87 17 E7 B7 B7 97 9B DB 47 CA DB DC 3F _.g........G...? +0224: 52 DE E6 7E 98 BC AB CB C7 0A BC BA 7C 92 C4 4F R..~........|..O +0240: 9B EB 42 D5 16 9F D4 2B A5 6C C5 3D 48 62 D1 AA ..B....+.l.=Hb.. +0256: 7B 98 C4 B2 95 87 CA FC BC F9 72 F9 FB 90 4A FB {.........r...J. +0272: CE 3D E0 DD FD E9 4F D8 73 0B 55 53 BF 8C 32 15 .=....O.s.US..2. +0288: 93 91 B1 78 FF 3E 3D 7D 16 9E FE F1 FE F6 F2 FA ...x.>=}........ +0304: 53 F3 E1 DF FE 7A 7D E1 3E 9D 7F 39 3C BF BE BE S....z}.>..9<... +0320: B9 3F 77 FF 71 37 3F FC EB 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job_out.672.d/out/tmp_672.vcf.gz job_out.673.d/out/tmp_673.vcf.gz job_out.674.d/out/tmp_674.vcf.gz job_out.675.d/out/tmp_675.vcf.gz job_out.676.d/out/tmp_676.vcf.gz job_out.677.d/out/tmp_677.vcf.gz job_out.678.d/out/tmp_678.vcf.gz job_out.679.d/out/tmp_679.vcf.gz job_out.680.d/out/tmp_680.vcf.gz job_out.681.d/out/tmp_681.vcf.gz job_out.682.d/out/tmp_682.vcf.gz job_out.683.d/out/tmp_683.vcf.gz job_out.684.d/out/tmp_684.vcf.gz job_out.685.d/out/tmp_685.vcf.gz job_out.686.d/out/tmp_686.vcf.gz job_out.687.d/out/tmp_687.vcf.gz job_out.688.d/out/tmp_688.vcf.gz job_out.689.d/out/tmp_689.vcf.gz job_out.690.d/out/tmp_690.vcf.gz job_out.691.d/out/tmp_691.vcf.gz job_out.692.d/out/tmp_692.vcf.gz; Date=Fri Aug 26 22:36:04 2022 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Case_1_father-N1-DNA1-WGS1 Case_1_index-N1-DNA1-WGS1 Case_1_mother-N1-DNA1-WGS1 +17 41249263 rs1799965 G A 573.13 . AC=1;AF=0.167;AN=6;BaseQRankSum=1.38;ClippingRankSum=0;DB;DP=140;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.167;MQ=60;MQRankSum=0;QD=13.65;ReadPosRankSum=-0.249;SOR=0.766 GT:AD:DP:GQ:PL 0/0:52,0:52:99:0,156,1718 0/0:46,0:46:99:0,138,1589 0/1:21,21:42:99:604,0,604 +17 41252332 rs781576075 T C 945.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=-0.53;ClippingRankSum=0;DB;DP=93;ExcessHet=3.9794;FS=0.806;MLEAC=2;MLEAF=0.333;MQ=60;MQRankSum=0;QD=13.9;ReadPosRankSum=1.905;SOR=0.557 GT:AD:DP:GQ:PL 0/0:25,0:25:75:0,75,849 0/1:14,14:28:99:392,0,403 0/1:19,21:40:99:585,0,539 +17 41252691 . ATATAAT A 614.13 . AC=2;AF=0.333;AN=6;BaseQRankSum=0;ClippingRankSum=0;DP=56;ExcessHet=3.9794;FS=4.119;MLEAC=2;MLEAF=0.333;MQ=60;MQRankSum=0;QD=16.6;ReadPosRankSum=-1.059;SOR=1.188 GT:AD:DP:GQ:PL 0/0:9,0:9:27:0,27,405 0/1:4,10:14:99:321,0,138 0/1:12,11:23:99:334,0,360 +17 41252693 rs377466939 ATAAT A 285.1 . AC=1;AF=0.167;AN=6;BaseQRankSum=0.621;ClippingRankSum=0;DB;DP=56;ExcessHet=3.0103;FS=1.37;MLEAC=1;MLEAF=0.167;MQ=60;MQRankSum=0;QD=12.96;ReadPosRankSum=-0.885;SOR=1.115 GT:AD:DP:GQ:PL 0/0:9,0:9:27:0,27,349 0/0:14,0:14:42:0,42,543 0/1:11,11:22:99:325,0,337 +17 41252695 rs56679756 AAT A 144.09 . AC=1;AF=0.167;AN=6;BaseQRankSum=0.458;ClippingRankSum=0;DB;DP=56;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.167;MQ=60;MQRankSum=0;QD=16.01;ReadPosRankSum=2.99;SOR=0.478 GT:AD:DP:GQ:PL 0/1:3,6:9:79:184,0,79 0/0:14,0:14:42:0,42,571 0/0:22,0:22:66:0,66,876 +17 41252696 rs10445319 A T 144.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=0.491;ClippingRankSum=0;DB;DP=56;ExcessHet=3.9794;FS=6.692;MLEAC=2;MLEAF=0.333;MQ=60;MQRankSum=0;QD=6.27;ReadPosRankSum=0.439;SOR=1.492 GT:AD:DP:GQ:PL 0/1:6,3:9:78:78,0,185 0/1:10,4:14:98:98,0,381 0/0:22,0:22:67:0,67,964 +17 41252697 . A AT,ATT 3178.86 . 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AC=1;AF=0.167;AN=6;BaseQRankSum=2.899;ClippingRankSum=-0.001;DP=6730;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.167;MQ=60;MQRankSum=-0.001;QD=4.94;ReadPosRankSum=0.898;SOR=0.663 GT:AD:DP:GQ:PL 0/0:2660,0:2660:99:0,7994,91201 0/1:1680,508:2188:99:10845,0,50969 0/0:1851,0:1851:99:0,5557,63188 +MT 11204 rs201803443 T C 183666 . AC=4;AF=0.667;AN=6;BaseQRankSum=6.514;ClippingRankSum=-0.015;DB;DP=8553;ExcessHet=0.4576;FS=0;MLEAC=4;MLEAF=0.667;MQ=59.96;MQRankSum=2.593;QD=34.39;ReadPosRankSum=-6.507;SOR=0.665 GT:AD:DP:GQ:PL 0/0:3168,5:3173:99:0,9411,106928 1/1:0,2922:2922:99:100296,8776,0 1/1:0,2418:2418:99:83408,7267,0 +MT 11674 rs28358286 C T 167026 . AC=4;AF=0.667;AN=6;BaseQRankSum=2.538;ClippingRankSum=-0.016;DB;DP=7754;ExcessHet=0.4576;FS=0;MLEAC=4;MLEAF=0.667;MQ=58.56;MQRankSum=-26.225;QD=34.47;ReadPosRankSum=-6.727;SOR=0.689 GT:AD:DP:GQ:PL 0/0:2890,0:2890:99:0,8678,99225 1/1:0,2666:2666:99:91850,8010,0 1/1:1,2179:2180:99:75214,6545,0 +MT 11719 rs2853495 G A 181704 . AC=4;AF=0.667;AN=6;BaseQRankSum=2.012;ClippingRankSum=-0.016;DB;DP=8621;ExcessHet=0.4576;FS=1.122;MLEAC=4;MLEAF=0.667;MQ=58.72;MQRankSum=-26.852;QD=34.58;ReadPosRankSum=-2.878;SOR=0.775 GT:AD:DP:GQ:PL 0/0:3339,2:3341:99:0,9993,114829 1/1:0,3052:3052:99:105503,9166,0 1/1:0,2203:2203:99:76239,6625,0 +MT 11947 rs28359168 A G 138146 . AC=4;AF=0.667;AN=6;BaseQRankSum=-6.069;ClippingRankSum=-0.011;DB;DP=6674;ExcessHet=0.4576;FS=0;MLEAC=4;MLEAF=0.667;MQ=59.99;MQRankSum=1.198;QD=33.88;ReadPosRankSum=-3.658;SOR=0.672 GT:AD:DP:GQ:PL 0/0:2579,2:2581:99:0,7727,88892 1/1:0,2273:2273:99:77242,6825,0 1/1:0,1804:1804:99:60942,5416,0 +MT 12414 rs193302950 T C 147603 . AC=4;AF=0.667;AN=6;BaseQRankSum=10.932;ClippingRankSum=-0.001;DB;DP=7160;ExcessHet=0.4576;FS=0;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=-0.001;QD=34.49;ReadPosRankSum=0.393;SOR=0.65 GT:AD:DP:GQ:PL 0/0:2852,3:2855:99:0,8482,95556 1/1:1,2545:2546:99:87714,7616,0 1/1:0,1733:1733:99:59927,5208,0 +MT 12648 . A G 117695 . AC=4;AF=0.667;AN=6;BaseQRankSum=-0.891;ClippingRankSum=0.002;DP=5272;ExcessHet=0.4576;FS=0.548;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=0.002;QD=34.16;ReadPosRankSum=-3.778;SOR=0.739 GT:AD:DP:GQ:PL 0/0:1812,1:1813:99:0,5398,61087 1/1:2,1662:1664:99:56988,4945,0 1/1:4,1777:1781:99:60745,5214,0 +MT 12705 rs193302956 C T 129264 . AC=4;AF=0.667;AN=6;BaseQRankSum=-1.576;ClippingRankSum=-0.008;DB;DP=6157;ExcessHet=0.4576;FS=0.531;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=-0.008;QD=34.38;ReadPosRankSum=0.001;SOR=0.709 GT:AD:DP:GQ:PL 0/0:2359,10:2369:99:0,6679,80813 1/1:1,2137:2138:99:73546,6407,0 1/1:1,1621:1622:99:55756,4857,0 +MT 13406 . G A 18935.1 . AC=1;AF=0.167;AN=6;BaseQRankSum=4.892;ClippingRankSum=-0.001;DP=6741;ExcessHet=3.0103;FS=0.853;MLEAC=1;MLEAF=0.167;MQ=59.93;MQRankSum=1.557;QD=9.68;ReadPosRankSum=-3.763;SOR=0.717 GT:AD:DP:GQ:PL 0/0:2539,1:2540:99:0,7611,88829 0/0:2216,0:2216:99:0,6672,76749 0/1:1224,733:1957:99:18966,0,36219 +MT 13611 . A G 226523 . AC=4;AF=0.667;AN=6;BaseQRankSum=-0.715;ClippingRankSum=-0.018;DP=10456;ExcessHet=0.4576;FS=0.541;MLEAC=4;MLEAF=0.667;MQ=59.95;MQRankSum=3.806;QD=34.57;ReadPosRankSum=-3.084;SOR=0.749 GT:AD:DP:GQ:PL 0/0:3838,2:3840:99:0,11470,131432 1/1:0,3717:3717:99:128767,11180,0 1/1:1,2834:2835:99:97794,8490,0 +MT 13928 rs28359184 G C 158255 . AC=4;AF=0.667;AN=6;BaseQRankSum=-2.077;ClippingRankSum=-0.001;DB;DP=7572;ExcessHet=0.4576;FS=0.537;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=-0.001;QD=34.55;ReadPosRankSum=0.177;SOR=0.614 GT:AD:DP:GQ:PL 0/0:2947,0:2947:99:0,8798,100755 1/1:0,2700:2700:99:93028,8117,0 1/1:0,1880:1880:99:65265,5652,0 +MT 14148 rs28357668 A G 163476 . AC=4;AF=0.667;AN=6;BaseQRankSum=-0.068;ClippingRankSum=-0.002;DB;DP=7865;ExcessHet=0.4576;FS=0;MLEAC=4;MLEAF=0.667;MQ=59.96;MQRankSum=3.807;QD=34.19;ReadPosRankSum=1.224;SOR=0.702 GT:AD:DP:GQ:PL 0/0:3019,2:3021:99:0,9046,102891 1/1:0,2820:2820:99:96517,8442,0 1/1:0,1962:1962:99:66997,5890,0 +MT 14766 rs527236041 C T 184246 . AC=4;AF=0.667;AN=6;BaseQRankSum=-4.916;ClippingRankSum=-0.016;DB;DP=8840;ExcessHet=0.4576;FS=1.797;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=-0.93;QD=33.68;ReadPosRankSum=-8.259;SOR=0.565 GT:AD:DP:GQ:PL 0/0:3318,3:3321:99:0,9897,113210 1/1:2,3111:3113:99:104758,9287,0 1/1:3,2355:2358:99:79526,6992,0 +MT 15326 rs2853508 A G 351443 . AC=6;AF=1;AN=6;DB;DP=9986;ExcessHet=3.0103;FS=0;MLEAC=6;MLEAF=1;MQ=60;QD=23.43;SOR=0.788 GT:AD:DP:GQ:PL 1/1:0,3716:3716:99:131483,11200,0 1/1:0,3560:3560:99:125277,10713,0 1/1:0,2690:2690:99:94709,8122,0 +MT 15884 . G C 203141 . AC=4;AF=0.667;AN=6;BaseQRankSum=1.841;ClippingRankSum=-0.02;DP=9526;ExcessHet=0.4576;FS=0;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=-0.02;QD=34.42;ReadPosRankSum=-6.501;SOR=0.721 GT:AD:DP:GQ:PL 0/0:3595,1:3596:99:0,10754,123245 1/1:0,3167:3167:99:109155,9521,0 1/1:1,2733:2734:99:94024,8195,0 +MT 16184 rs34100702 C T 118028 . AC=4;AF=0.667;AN=6;BaseQRankSum=3.32;ClippingRankSum=0;DB;DP=4885;ExcessHet=0.4576;FS=3.599;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=0;QD=34.24;ReadPosRankSum=2.363;SOR=0.93 GT:AD:DP:GQ:PL 0/0:1406,1:1407:99:0,4183,47484 1/1:0,1969:1969:99:67640,5881,0 1/1:0,1478:1478:99:50426,4408,0 +MT 16223 rs2853513 C T 120350 . AC=4;AF=0.667;AN=6;BaseQRankSum=0.452;ClippingRankSum=-0.001;DB;DP=4936;ExcessHet=0.4576;FS=8.04;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=-0.001;QD=34.48;ReadPosRankSum=0.914;SOR=1.051 GT:AD:DP:GQ:PL 0/0:1405,1:1406:99:0,4181,48090 1/1:0,2018:2018:99:69507,6063,0 1/1:0,1472:1472:99:50881,4420,0 +MT 16263 . T C 50770.1 . AC=2;AF=0.333;AN=6;BaseQRankSum=-1.81;ClippingRankSum=0;DP=5017;ExcessHet=0.4576;FS=18.084;MLEAC=2;MLEAF=0.333;MQ=60;MQRankSum=0;QD=34.35;ReadPosRankSum=-1.303;SOR=0.23 GT:AD:DP:GQ:PL 1/1:2,1476:1478:99:50817,4422,0 0/0:1994,0:1994:99:0,5989,69016 0/0:1475,0:1475:99:0,4439,51221 +MT 16292 rs144417390 C T 113132 . AC=4;AF=0.667;AN=6;BaseQRankSum=-7.684;ClippingRankSum=-0.001;DB;DP=5092;ExcessHet=0.4576;FS=26.574;MLEAC=4;MLEAF=0.667;MQ=60;MQRankSum=-0.001;QD=33.37;ReadPosRankSum=4.375;SOR=2.115 GT:AD:DP:GQ:PL 0/0:1652,0:1652:99:0,4962,57207 1/1:1,1913:1914:99:63339,5702,0 1/1:0,1476:1476:99:49831,4419,0 +MT 16519 rs3937033 T C 263844 . AC=6;AF=1;AN=6;DB;DP=7636;ExcessHet=3.0103;FS=0;MLEAC=6;MLEAF=1;MQ=60;QD=34.73;SOR=3.902 GT:AD:DP:GQ:PL 1/1:0,1759:1759:99:61243,5289,0 1/1:0,4094:4094:99:142289,12314,0 1/1:0,1744:1744:99:60338,5251,0 diff --git a/tests/seqvars/ingest/NA12878_dragen.ped b/tests/seqvars/ingest/NA12878_dragen.ped new file mode 100644 index 00000000..ee57fd24 --- /dev/null +++ b/tests/seqvars/ingest/NA12878_dragen.ped @@ -0,0 +1 @@ +FAM NA12878 0 0 2 2 diff --git a/tests/seqvars/ingest/NA12878_dragen.vcf b/tests/seqvars/ingest/NA12878_dragen.vcf new file mode 100644 index 00000000..d1a8c95a --- /dev/null +++ b/tests/seqvars/ingest/NA12878_dragen.vcf @@ -0,0 +1,247 @@ +##fileformat=VCFv4.2 +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##DRAGENCommandLine= +##DRAGENCommandLine= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##contig= +##reference=file:///staging/human/reference/hs37d5/hs37d5.fa.k_21.f_16.m_149/reference.bin +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 +17 41244000 . T C 50.00 . AC=1;AF=0.500;AN=2;DP=26;FS=6.648;MQ=250.00;MQRankSum=3.972;QD=1.92;ReadPosRankSum=2.306;SOR=0.517;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:8,18:0.692:26:3,10:5,8:43:85,0,41:5.0000e+01,2.1964e-04,4.3917e+01:0.00,34.77,37.77:6,2,8,10:5,3,6,12 +17 41244435 . T C 50.00 . AC=1;AF=0.500;AN=2;DP=26;FS=1.540;MQ=250.00;MQRankSum=4.295;QD=1.92;ReadPosRankSum=3.266;SOR=0.412;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:12,14:0.538:26:6,4:6,10:47:85,0,47:5.0000e+01,8.8200e-05,4.9868e+01:0.00,34.77,37.78:4,8,6,8:6,6,10,4 +17 41244936 . G A 48.84 . AC=1;AF=0.500;AN=2;DP=30;FS=1.484;MQ=250.00;MQRankSum=4.604;QD=1.63;ReadPosRankSum=1.841;SOR=0.368;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:17,13:0.433:30:9,9:8,4:47:84,0,50:4.8838e+01,7.8515e-05,5.3000e+01:0.00,34.77,37.77:11,6,7,6:7,10,7,6 +17 41245237 . A G 46.47 . AC=1;AF=0.500;AN=2;DP=29;FS=8.457;MQ=250.00;MQRankSum=4.427;QD=1.60;ReadPosRankSum=2.135;SOR=1.047;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:18,11:0.379:29:5,8:13,3:46:81,0,50:4.6469e+01,1.1970e-04,5.3000e+01:0.00,34.77,37.77:6,12,7,4:11,7,6,5 +17 41245466 . G A 48.96 . AC=1;AF=0.500;AN=2;DP=19;FS=7.425;MQ=250.00;MQRankSum=3.592;QD=2.58;ReadPosRankSum=2.849;SOR=0.895;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:11,8:0.421:19:6,3:5,5:48:84,0,50:4.8964e+01,7.6898e-05,5.3000e+01:0.00,34.77,37.77:8,3,3,5:5,6,4,4 +17 41247122 . A ACCT 46.28 . AC=1;AF=0.500;AN=2;DP=30;FS=1.571;MQ=250.00;MQRankSum=4.427;QD=1.54;ReadPosRankSum=-0.382;SOR=0.333;FractionInformativeReads=0.967 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:18,11:0.379:29:13,5:5,6:45:75,0,50:4.6283e+01,1.2397e-04,5.3000e+01:0.00,29.00,32.00:6,12,5,6:7,11,7,4 +17 41247604 . A C 49.91 . AC=1;AF=0.500;AN=2;DP=23;FS=0.000;MQ=245.42;MQRankSum=3.416;QD=2.17;ReadPosRankSum=-0.831;SOR=0.859;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:12,11:0.478:23:5,8:7,3:47:85,0,47:4.9907e+01,8.7803e-05,5.0000e+01:0.00,34.77,37.78:6,6,5,6:7,5,2,9 +17 41248164 . C T 44.42 . AC=1;AF=0.500;AN=2;DP=21;FS=0.000;MQ=213.09;MQRankSum=-2.648;QD=2.12;ReadPosRankSum=2.574;SOR=0.941;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:14,7:0.333:21:10,5:4,2:44:79,0,50:4.4419e+01,1.7876e-04,5.3000e+01:0.00,34.77,37.77:7,7,3,4:3,11,3,4 +17 41248393 . C CAAAAAAAAAA 49.40 . AC=1;AF=0.500;AN=2;DP=17;FS=0.000;MQ=235.18;MQRankSum=-0.529;QD=2.91;ReadPosRankSum=-0.212;SOR=0.814;FractionInformativeReads=0.941 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:9,7:0.438:16:5,7:4,0:48:55,0,50:4.9403e+01,7.1595e-05,5.3000e+01:0.00,6.00,9.00:4,5,4,3:2,7,4,3 +17 41248484 . G C 49.57 . AC=1;AF=0.500;AN=2;DP=20;FS=0.000;MQ=246.56;MQRankSum=2.051;QD=2.48;ReadPosRankSum=-0.532;SOR=0.787;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:11,9:0.450:20:6,8:5,1:48:84,0,50:4.9565e+01,6.9766e-05,5.3000e+01:0.00,34.77,37.77:4,7,3,6:5,6,4,5 +17 41248588 . CA C 43.90 . AC=1;AF=0.500;AN=2;DP=20;FS=0.000;MQ=249.95;MQRankSum=2.899;QD=2.20;ReadPosRankSum=-0.531;SOR=0.495;FractionInformativeReads=0.950 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:9,10:0.526:19:5,6:4,4:42:50,0,44:4.3903e+01,2.6733e-04,4.6810e+01:0.00,6.00,9.00:3,6,4,6:7,2,4,6 +17 41249094 . A G 49.46 . AC=1;AF=0.500;AN=2;DP=16;FS=0.000;MQ=250.00;MQRankSum=3.281;QD=3.09;ReadPosRankSum=2.540;SOR=0.836;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:9,7:0.438:16:6,5:3,2:48:84,0,50:4.9456e+01,7.0997e-05,5.3000e+01:0.00,34.77,37.77:3,6,2,5:4,5,4,3 +17 41249363 . TA T 50.00 . AC=1;AF=0.500;AN=2;DP=27;FS=0.000;MQ=250.00;MQRankSum=4.215;QD=1.85;ReadPosRankSum=-0.517;SOR=0.551;FractionInformativeReads=0.926 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:12,13:0.520:25:6,9:6,4:48:75,0,50:5.0000e+01,6.5634e-05,5.2913e+01:0.00,25.00,28.00:7,5,7,6:5,7,5,8 +17 41250047 . C CT 17.50 . AC=1;AF=0.500;AN=2;DP=23;FS=0.000;MQ=246.77;MQRankSum=3.566;QD=0.76;ReadPosRankSum=0.792;SOR=0.787;FractionInformativeReads=0.870 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:13,7:0.350:20:9,1:4,6:18:24,0,50:1.7502e+01,7.7909e-02,5.3078e+01:0.00,7.00,10.00:7,6,4,3:11,2,4,3 +17 41250678 . C CT 50.00 . AC=1;AF=0.500;AN=2;DP=22;FS=0.000;MQ=250.00;MQRankSum=3.502;QD=2.27;ReadPosRankSum=-0.111;SOR=0.446;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:6,16:0.727:22:2,11:4,5:42:79,0,40:5.0000e+01,2.7332e-04,4.2763e+01:0.00,29.00,32.00:2,4,7,9:2,4,8,8 +17 41250923 . T C 48.55 . AC=1;AF=0.500;AN=2;DP=22;FS=4.200;MQ=215.51;MQRankSum=-1.536;QD=2.21;ReadPosRankSum=0.067;SOR=1.863;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:13,9:0.409:22:7,5:6,4:47:83,0,50:4.8551e+01,8.2395e-05,5.3000e+01:0.00,34.77,37.77:6,7,2,7:8,5,6,3 +17 41251495 . C G 50.00 . AC=1;AF=0.500;AN=2;DP=26;FS=0.000;MQ=244.58;MQRankSum=0.830;QD=1.92;ReadPosRankSum=2.284;SOR=0.586;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:11,15:0.577:26:5,5:6,10:48:85,0,49:5.0000e+01,7.3065e-05,5.1660e+01:0.00,34.77,37.77:4,7,6,9:6,5,8,7 +17 41251646 . T A 48.97 . AC=1;AF=0.500;AN=2;DP=19;FS=0.000;MQ=250.00;MQRankSum=3.592;QD=2.58;ReadPosRankSum=2.766;SOR=0.976;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:11,8:0.421:19:6,4:5,4:48:84,0,50:4.8967e+01,7.6857e-05,5.3000e+01:0.00,34.77,37.77:5,6,3,5:4,7,3,5 +17 41252575 . G A 54.75 . AC=2;AF=1.000;AN=2;DP=4;FS=0.000;MQ=248.67;QD=13.69;SOR=2.833;FractionInformativeReads=0.750 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB:PS 1|1:0,3:1.000:3:0,3:0,0:5:91,6,0:5.4747e+01,4.7465e+00,1.7733e+00:0.00,34.77,37.78:0,0,0,3:0,0,0,3:41252575 +17 41252591 . C CAT 34.86 . AC=2;AF=1.000;AN=2;DP=3;FS=0.000;MQ=248.01;QD=11.62;SOR=2.303;FractionInformativeReads=0.667 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB:PS 1|1:0,2:1.000:2:0,2:0,0:4:63,4,0:3.4859e+01,3.5093e+00,2.5654e+00:0.00,28.00,31.01:0,0,0,2:0,0,0,2:41252575 +17 41254174 . A G 49.92 . AC=1;AF=0.500;AN=2;DP=27;FS=0.000;MQ=214.81;MQRankSum=1.189;QD=1.85;ReadPosRankSum=0.024;SOR=0.593;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:14,13:0.481:27:7,6:7,7:48:85,0,50:4.9920e+01,6.6004e-05,5.3000e+01:0.00,34.77,37.77:5,9,5,8:6,8,6,7 +17 41254374 . C CTTTTTTTT 50.00 . AC=1;AF=0.500;AN=2;DP=16;FS=5.434;MQ=210.96;MQRankSum=-0.660;QD=3.13;ReadPosRankSum=-0.811;SOR=1.472;FractionInformativeReads=0.812 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:6,7:0.538:13:3,2:3,5:48:56,0,50:5.0000e+01,6.6039e-05,5.2835e+01:0.00,6.00,9.00:4,2,2,5:3,3,3,4 +17 41254405 . C T 49.85 . AC=1;AF=0.500;AN=2;DP=18;FS=5.880;MQ=194.63;MQRankSum=-1.867;QD=2.77;ReadPosRankSum=-1.200;SOR=0.082;FractionInformativeReads=0.778 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:5,9:0.643:14:2,4:3,5:43:85,0,41:4.9850e+01,2.2411e-04,4.3846e+01:0.00,34.77,37.77:0,5,3,6:3,2,6,3 +17 41254486 . T G 50.00 . AC=1;AF=0.500;AN=2;DP=24;FS=0.000;MQ=190.76;MQRankSum=-2.872;QD=2.08;ReadPosRankSum=2.033;SOR=0.446;FractionInformativeReads=0.958 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:8,15:0.652:23:2,8:6,7:46:85,0,45:5.0000e+01,1.0767e-04,4.8300e+01:0.00,34.77,37.77:3,5,7,8:5,3,8,7 +17 41254965 . C CT 21.87 . AC=1;AF=0.500;AN=2;DP=27;FS=6.897;MQ=250.00;MQRankSum=3.788;QD=0.81;ReadPosRankSum=-0.512;SOR=1.800;FractionInformativeReads=0.815 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:14,8:0.364:22:7,5:7,3:22:31,0,50:2.1869e+01,2.8358e-02,5.3028e+01:0.00,9.00,12.00:6,8,6,2:5,9,5,3 +17 41255102 . A G 46.54 . AC=1;AF=0.500;AN=2;DP=31;FS=8.915;MQ=250.00;MQRankSum=4.603;QD=1.50;ReadPosRankSum=2.656;SOR=2.494;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB:PS 0|1:19,12:0.387:31:11,3:8,9:46:81,0,50:4.6540e+01,1.1810e-04,5.3000e+01:0.00,34.77,37.77:10,9,10,2:8,11,3,9:41255102 +17 41255111 . A T 46.54 . AC=1;AF=0.500;AN=2;DP=31;FS=8.915;MQ=250.00;MQRankSum=4.603;QD=1.50;ReadPosRankSum=3.305;SOR=2.494;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB:PS 0|1:19,12:0.387:31:12,3:7,9:46:81,0,50:4.6540e+01,1.1809e-04,5.3000e+01:0.00,34.77,37.77:10,9,10,2:7,12,3,9:41255102 +17 41256074 . CA C 44.34 . AC=1;AF=0.500;AN=2;DP=18;FS=0.000;MQ=243.16;MQRankSum=3.266;QD=2.46;ReadPosRankSum=2.663;SOR=1.112;FractionInformativeReads=0.944 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB:PS 0|1:11,6:0.353:17:8,3:3,3:43:55,0,47:4.4342e+01,2.0325e-04,5.0000e+01:0.00,11.00,14.01:5,6,2,4:4,7,5,1:41256074 +17 41256089 . AAAAAAAAAGAAAAG A 44.34 . AC=1;AF=0.500;AN=2;DP=19;FS=1.808;MQ=243.52;MQRankSum=3.377;QD=2.33;ReadPosRankSum=2.412;SOR=1.140;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB:PS 0|1:13,6:0.316:19:8,3:5,3:43:59,0,47:4.4345e+01,2.0313e-04,5.0000e+01:0.00,15.00,18.01:6,7,2,4:5,8,5,1:41256074 +17 41257134 . T C 50.00 . AC=1;AF=0.500;AN=2;DP=29;FS=1.550;MQ=250.00;MQRankSum=4.561;QD=1.72;ReadPosRankSum=0.982;SOR=1.123;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:14,15:0.517:29:4,10:10,5:48:85,0,50:5.0000e+01,6.5568e-05,5.2926e+01:0.00,34.77,37.77:9,5,11,4:5,9,6,9 +17 41257458 . A C 50.00 . AC=1;AF=0.500;AN=2;DP=26;FS=0.000;MQ=250.00;MQRankSum=4.256;QD=1.92;ReadPosRankSum=1.972;SOR=0.586;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:11,15:0.577:26:5,7:6,8:48:85,0,49:5.0000e+01,7.2281e-05,5.1776e+01:0.00,34.77,37.77:4,7,6,9:6,5,6,9 +17 41258043 . C T 49.92 . AC=1;AF=0.500;AN=2;DP=27;FS=1.510;MQ=245.17;MQRankSum=3.761;QD=1.85;ReadPosRankSum=2.499;SOR=0.648;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:14,13:0.481:27:10,4:4,9:48:85,0,50:4.9921e+01,6.5994e-05,5.3000e+01:0.00,34.77,37.77:6,8,7,6:10,4,8,5 +17 41258135 . T TA 53.60 . AC=2;AF=1.000;AN=2;DP=18;FS=2.688;MQ=245.55;MQRankSum=1.557;QD=2.98;ReadPosRankSum=-0.623;SOR=1.100;FractionInformativeReads=0.778 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 1/1:3,11:0.786:14:3,5:0,6:4:60,4,0:5.3602e+01,3.6018e+00,2.4898e+00:0.00,6.00,9.00:1,2,7,4:1,2,7,4 +17 41259049 . C T 50.00 . AC=1;AF=0.500;AN=2;DP=16;FS=0.000;MQ=243.62;MQRankSum=2.468;QD=3.13;ReadPosRankSum=-1.208;SOR=0.693;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:8,8:0.500:16:4,4:4,4:48:85,0,50:5.0000e+01,6.5195e-05,5.3000e+01:0.00,34.77,37.77:3,5,3,5:5,3,5,3 +17 41259079 . A ATT 6.69 . AC=1;AF=0.500;AN=2;DP=17;FS=0.000;MQ=201.18;MQRankSum=-1.944;QD=0.39;ReadPosRankSum=-0.254;SOR=0.765;FractionInformativeReads=0.765 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:10,3:0.231:13:7,0:3,3:7:11,0,50:6.6138e+00,1.0684e+00,5.4068e+01:0.00,5.00,8.00:4,6,1,2:5,5,2,1 +17 41259113 . G A 49.21 . AC=1;AF=0.500;AN=2;DP=20;FS=1.820;MQ=165.08;MQRankSum=-2.931;QD=2.46;ReadPosRankSum=-1.032;SOR=0.330;FractionInformativeReads=0.950 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:11,8:0.421:19:8,2:3,6:48:84,0,50:4.9209e+01,7.3869e-05,5.3000e+01:0.00,34.77,37.77:7,4,4,4:8,3,4,4 +17 41260352 . C CA 43.45 . AC=1;AF=0.500;AN=2;DP=24;FS=0.000;MQ=249.39;MQRankSum=2.684;QD=1.81;ReadPosRankSum=-0.206;SOR=0.551;FractionInformativeReads=0.792 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:11,8:0.421:19:6,5:5,3:43:52,0,50:4.3451e+01,2.1797e-04,5.3000e+01:0.00,9.00,12.00:6,5,4,4:5,6,5,3 +17 41260723 . C CAAAAA 21.36 . AC=1;AF=0.500;AN=2;DP=3;FS=0.000;MQ=180.17;MQRankSum=0.804;QD=7.12;ReadPosRankSum=0.804;SOR=0.693;FractionInformativeReads=0.667 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:1,1:0.500:2:1,1:0,0:20:26,0,25:2.1156e+01,4.0776e-02,2.7744e+01:0.00,5.00,8.00:1,0,1,0:1,0,1,0 +17 41260808 . A G 32.31 . AC=1;AF=0.500;AN=2;DP=16;FS=2.963;MQ=226.56;MQRankSum=-1.804;QD=2.02;ReadPosRankSum=-1.227;SOR=2.303;FractionInformativeReads=0.938 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:12,3:0.200:15:9,2:3,1:32:67,0,50:3.2315e+01,2.5712e-03,5.3003e+01:0.00,34.77,37.77:7,5,3,0:6,6,2,1 +17 41261058 . T TCTATCTATCTACCTAC 50.00 . AC=1;AF=0.500;AN=2;DP=22;FS=8.038;MQ=245.59;MQRankSum=1.671;QD=2.27;ReadPosRankSum=0.228;SOR=0.065;FractionInformativeReads=0.909 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:9,11:0.550:20:7,5:2,6:48:79,0,50:5.0000e+01,6.7276e-05,5.2604e+01:0.00,29.00,32.00:1,8,5,6:3,6,5,6 +17 41261233 . C T 50.00 . AC=1;AF=0.500;AN=2;DP=27;FS=3.473;MQ=249.57;MQRankSum=3.782;QD=1.85;ReadPosRankSum=1.586;SOR=0.957;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:12,15:0.556:27:5,7:7,8:48:85,0,49:5.0000e+01,6.8635e-05,5.2363e+01:0.00,34.77,37.77:5,7,9,6:8,4,7,8 +17 41263044 . A G 50.00 . AC=1;AF=0.500;AN=2;DP=17;FS=0.000;MQ=211.79;MQRankSum=-1.154;QD=2.94;ReadPosRankSum=1.027;SOR=0.283;FractionInformativeReads=0.824 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:7,7:0.500:14:3,4:4,3:48:85,0,50:5.0000e+01,6.5195e-05,5.3000e+01:0.00,34.77,37.77:6,1,5,2:2,5,4,3 +17 41263117 . C CA 33.78 . AC=1;AF=0.500;AN=2;DP=24;FS=0.000;MQ=241.08;MQRankSum=1.147;QD=1.41;ReadPosRankSum=0.899;SOR=0.569;FractionInformativeReads=0.958 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:13,10:0.435:23:6,6:7,4:34:41,0,50:3.3776e+01,1.8426e-03,5.3002e+01:0.00,7.00,10.00:6,7,5,5:7,6,5,5 +17 41263566 . T C 48.97 . AC=1;AF=0.500;AN=2;DP=19;FS=11.311;MQ=236.39;MQRankSum=0.041;QD=2.58;ReadPosRankSum=3.592;SOR=0.850;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:11,8:0.421:19:5,5:6,3:48:84,0,50:4.8967e+01,7.6857e-05,5.3000e+01:0.00,34.77,37.77:2,9,5,3:8,3,4,4 +17 41264146 . G A 46.03 . AC=1;AF=0.500;AN=2;DP=20;FS=1.922;MQ=249.51;MQRankSum=3.566;QD=2.30;ReadPosRankSum=2.060;SOR=0.697;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:13,7:0.350:20:9,5:4,2:45:81,0,50:4.6029e+01,1.3012e-04,5.3000e+01:0.00,34.77,37.77:8,5,3,4:6,7,5,2 +17 41264364 . A G 50.00 . AC=1;AF=0.500;AN=2;DP=24;FS=9.582;MQ=242.19;MQRankSum=1.439;QD=2.08;ReadPosRankSum=2.296;SOR=0.976;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:8,16:0.667:24:4,10:4,6:45:85,0,44:5.0000e+01,1.3668e-04,4.6681e+01:0.00,34.77,37.77:6,2,6,10:6,2,4,12 +17 41264739 . C T 50.00 . AC=1;AF=0.500;AN=2;DP=29;FS=3.315;MQ=245.44;MQRankSum=2.728;QD=1.72;ReadPosRankSum=0.458;SOR=0.973;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB:PS 0|1:14,15:0.517:29:8,9:6,6:48:85,0,50:5.0000e+01,6.5568e-05,5.2926e+01:0.00,34.77,37.77:8,6,6,9:10,4,4,11:41264739 +17 41264740 . TGA T 50.00 . AC=1;AF=0.500;AN=2;DP=30;FS=1.455;MQ=245.59;MQRankSum=2.889;QD=1.67;ReadPosRankSum=0.104;SOR=0.774;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:14,16:0.533:30:8,10:6,6:48:79,0,50:5.0000e+01,6.6695e-05,5.2711e+01:0.00,29.00,32.00:8,6,7,9:10,4,5,11 +17 41264743 . CT C 50.00 . AC=1;AF=0.500;AN=2;DP=29;FS=1.455;MQ=245.44;MQRankSum=2.728;QD=1.72;ReadPosRankSum=0.371;SOR=0.626;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB:PS 0|1:14,15:0.517:29:8,9:6,6:48:79,0,50:5.0000e+01,6.5414e-05,5.2957e+01:0.00,29.00,32.00:8,6,7,8:10,4,5,10:41264739 +17 41264749 . C G 50.00 . AC=1;AF=0.500;AN=2;DP=29;FS=0.000;MQ=245.44;MQRankSum=2.728;QD=1.72;ReadPosRankSum=-0.022;SOR=0.818;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB:PS 0|1:14,15:0.517:29:8,9:6,6:48:85,0,50:5.0000e+01,6.5568e-05,5.2926e+01:0.00,34.77,37.77:7,7,7,8:9,5,5,10:41264739 +17 41264750 . A T 50.00 . AC=1;AF=0.500;AN=2;DP=29;FS=1.455;MQ=245.44;MQRankSum=2.728;QD=1.72;ReadPosRankSum=-0.240;SOR=0.626;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB:PS 0|1:14,15:0.517:29:8,9:6,6:48:85,0,50:5.0000e+01,6.5723e-05,5.2896e+01:0.00,34.77,37.77:8,6,7,8:10,4,5,10:41264739 +17 41264751 . A AGGG 50.00 . AC=1;AF=0.500;AN=2;DP=29;FS=1.455;MQ=245.44;MQRankSum=2.728;QD=1.72;ReadPosRankSum=-0.022;SOR=0.626;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB:PS 0|1:14,15:0.517:29:8,9:6,6:48:79,0,50:5.0000e+01,6.5567e-05,5.2927e+01:0.00,29.00,32.00:8,6,7,8:10,4,5,10:41264739 +17 41264753 . C T 49.95 . AC=1;AF=0.500;AN=2;DP=27;FS=0.000;MQ=245.10;MQRankSum=2.354;QD=1.85;ReadPosRankSum=0.655;SOR=0.836;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB:PS 0|1:14,13:0.481:27:8,7:6,6:48:85,0,50:4.9952e+01,6.5680e-05,5.3000e+01:0.00,34.77,37.77:7,7,7,6:9,5,5,8:41264739 +17 41264755 . TGAAAC T 49.92 . AC=1;AF=0.500;AN=2;DP=27;FS=0.000;MQ=245.10;MQRankSum=2.354;QD=1.85;ReadPosRankSum=0.898;SOR=0.836;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB:PS 0|1:14,13:0.481:27:8,7:6,6:48:79,0,50:4.9920e+01,6.6000e-05,5.3000e+01:0.00,29.00,32.00:7,7,7,6:9,5,5,8:41264739 +17 41265776 . A G 44.93 . AC=1;AF=0.500;AN=2;DP=37;FS=1.323;MQ=250.00;MQRankSum=5.026;QD=1.21;ReadPosRankSum=1.926;SOR=0.918;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:23,14:0.378:37:13,5:10,9:44:80,0,50:4.4928e+01,1.6140e-04,5.3000e+01:0.00,34.77,37.77:12,11,6,8:18,5,7,7 +17 41266407 . C CT 32.74 . AC=1;AF=0.500;AN=2;DP=20;FS=7.259;MQ=250.00;MQRankSum=3.510;QD=1.64;ReadPosRankSum=0.222;SOR=1.784;FractionInformativeReads=0.900 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:10,8:0.444:18:3,3:7,5:33:40,0,50:3.2743e+01,2.3317e-03,5.3002e+01:0.00,7.00,10.00:4,6,6,2:7,3,3,5 +17 41267050 . G A 50.00 . AC=1;AF=0.500;AN=2;DP=23;FS=0.000;MQ=250.00;MQRankSum=3.708;QD=2.17;ReadPosRankSum=0.902;SOR=0.948;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:7,16:0.696:23:2,8:5,8:44:85,0,42:5.0000e+01,1.7612e-04,4.5150e+01:0.00,34.77,37.77:4,3,10,6:3,4,8,8 +17 41267518 . CA C 34.60 . AC=1;AF=0.500;AN=2;DP=19;FS=0.000;MQ=249.03;MQRankSum=2.684;QD=1.82;ReadPosRankSum=1.528;SOR=0.551;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:11,8:0.421:19:5,7:6,1:35:43,0,50:3.4597e+01,1.5289e-03,5.3002e+01:0.00,8.00,11.00:6,5,4,4:2,9,3,5 +17 41268206 . A C 47.63 . AC=1;AF=0.500;AN=2;DP=22;FS=0.000;MQ=250.00;MQRankSum=3.873;QD=2.17;ReadPosRankSum=0.467;SOR=0.743;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB:PS 0|1:13,9:0.409:22:8,6:5,3:46:82,0,47:4.7633e+01,1.1833e-04,5.0000e+01:0.00,34.77,37.78:6,7,4,5:5,8,7,2:41268206 +17 41268208 . C CT 47.63 . AC=1;AF=0.500;AN=2;DP=23;FS=0.000;MQ=250.00;MQRankSum=3.873;QD=2.07;ReadPosRankSum=0.601;SOR=0.791;FractionInformativeReads=0.957 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB:PS 0|1:13,9:0.409:22:9,6:4,3:46:69,0,47:4.7633e+01,1.1833e-04,5.0000e+01:0.00,21.00,24.01:7,6,4,5:5,8,7,2:41268206 +17 41270229 . T G 49.00 . AC=1;AF=0.500;AN=2;DP=24;FS=0.000;MQ=116.11;MQRankSum=-0.572;QD=2.04;ReadPosRankSum=2.096;SOR=0.582;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:7,17:0.708:24:4,7:3,10:40:84,0,38:4.9000e+01,4.1689e-04,4.0788e+01:0.00,34.77,37.77:3,4,8,9:4,3,10,7 +17 41270277 . C T 50.00 . AC=1;AF=0.500;AN=2;DP=22;FS=1.792;MQ=139.69;MQRankSum=-0.334;QD=2.27;ReadPosRankSum=1.202;SOR=1.329;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:9,13:0.591:22:4,6:5,7:48:85,0,49:5.0000e+01,7.3842e-05,5.1547e+01:0.00,34.77,37.77:4,5,4,9:3,6,7,6 +17 41270463 . G A 49.62 . AC=1;AF=0.500;AN=2;DP=29;FS=1.518;MQ=212.00;MQRankSum=1.474;QD=1.71;ReadPosRankSum=2.856;SOR=0.586;FractionInformativeReads=0.966 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:15,13:0.464:28:6,9:9,4:48:84,0,50:4.9621e+01,6.9157e-05,5.3000e+01:0.00,34.77,37.77:9,6,6,7:8,7,10,3 +17 41270666 . C A 42.91 . AC=1;AF=0.500;AN=2;DP=16;FS=0.000;MQ=226.92;MQRankSum=-0.457;QD=2.68;ReadPosRankSum=1.501;SOR=0.551;FractionInformativeReads=0.938 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:11,4:0.267:15:7,3:4,1:43:78,0,50:4.2913e+01,2.4386e-04,5.3000e+01:0.00,34.77,37.77:6,5,2,2:6,5,1,3 +17 41270778 . C CT 14.05 . AC=1;AF=0.500;AN=2;DP=19;FS=2.060;MQ=228.42;MQRankSum=0.793;QD=0.74;ReadPosRankSum=0.680;SOR=1.236;FractionInformativeReads=0.842 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:11,5:0.312:16:6,4:5,1:14:23,0,47:1.4053e+01,1.7430e-01,5.0174e+01:0.00,9.00,12.01:4,7,1,4:5,6,0,5 +17 41271293 . GA G 50.00 . AC=1;AF=0.500;AN=2;DP=21;FS=0.000;MQ=250.00;MQRankSum=3.742;QD=2.38;ReadPosRankSum=-0.265;SOR=0.693;FractionInformativeReads=0.952 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:10,10:0.500:20:5,2:5,8:48:60,0,50:5.0000e+01,6.5195e-05,5.3000e+01:0.00,10.00,13.00:4,6,4,6:9,1,4,6 +17 41273095 . G A 48.18 . AC=1;AF=0.500;AN=2;DP=20;FS=4.285;MQ=243.91;MQRankSum=2.739;QD=2.41;ReadPosRankSum=0.270;SOR=1.863;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:12,8:0.400:20:9,7:3,1:47:83,0,50:4.8185e+01,8.7728e-05,5.3000e+01:0.00,34.77,37.77:6,6,2,6:7,5,3,5 +17 41273348 . T C 48.08 . AC=1;AF=0.500;AN=2;DP=32;FS=3.352;MQ=212.50;MQRankSum=0.821;QD=1.50;ReadPosRankSum=-0.100;SOR=1.609;FractionInformativeReads=0.969 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:18,13:0.419:31:14,7:4,6:47:83,0,50:4.8079e+01,8.9364e-05,5.3000e+01:0.00,34.77,37.77:9,9,9,4:7,11,9,4 +17 41273379 . G C 48.35 . AC=1;AF=0.500;AN=2;DP=33;FS=5.093;MQ=232.68;MQRankSum=1.767;QD=1.47;ReadPosRankSum=2.932;SOR=1.609;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:19,14:0.424:33:13,6:6,8:47:83,0,50:4.8348e+01,8.5297e-05,5.3000e+01:0.00,34.77,37.77:10,9,10,4:8,11,8,6 +17 41273537 . A C 50.00 . AC=1;AF=0.500;AN=2;DP=33;FS=3.419;MQ=242.40;MQRankSum=1.184;QD=1.52;ReadPosRankSum=2.240;SOR=0.257;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:14,19:0.576:33:7,12:7,7:48:85,0,48:5.0000e+01,7.4433e-05,5.1464e+01:0.00,34.77,37.77:3,11,7,12:6,8,6,13 +17 41274778 . G A 50.00 . AC=1;AF=0.500;AN=2;DP=28;FS=0.000;MQ=249.53;MQRankSum=3.775;QD=1.79;ReadPosRankSum=1.604;SOR=0.765;FractionInformativeReads=0.964 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:11,16:0.593:27:6,11:5,5:48:85,0,48:5.0000e+01,7.5966e-05,5.1254e+01:0.00,34.77,37.77:5,6,7,9:6,5,8,8 +17 41274906 . G A 49.15 . AC=1;AF=0.500;AN=2;DP=27;FS=3.816;MQ=245.01;MQRankSum=1.029;QD=1.82;ReadPosRankSum=0.326;SOR=0.193;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:17,10:0.370:27:7,4:10,6:47:84,0,47:4.9145e+01,9.6306e-05,5.0000e+01:0.00,34.77,37.78:5,12,5,5:11,6,5,5 +17 41275081 . G GA 50.00 . AC=1;AF=0.500;AN=2;DP=23;FS=0.000;MQ=219.53;MQRankSum=-0.626;QD=2.17;ReadPosRankSum=0.165;SOR=1.022;FractionInformativeReads=0.957 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:10,12:0.545:22:4,5:6,7:47:67,0,47:5.0000e+01,9.1554e-05,4.9554e+01:0.00,17.00,20.01:5,5,7,5:3,7,6,6 +17 41275151 . G C 49.62 . AC=1;AF=0.500;AN=2;DP=29;FS=3.372;MQ=226.61;MQRankSum=2.902;QD=1.71;ReadPosRankSum=-0.461;SOR=1.426;FractionInformativeReads=0.966 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:15,13:0.464:28:6,8:9,5:48:84,0,50:4.9622e+01,6.9150e-05,5.3000e+01:0.00,34.77,37.77:7,8,4,9:10,5,7,6 +17 41275366 . GTTTTTTT G 50.00 . AC=1;AF=0.500;AN=2;DP=23;FS=4.123;MQ=243.51;MQRankSum=2.570;QD=2.17;ReadPosRankSum=-0.246;SOR=0.477;FractionInformativeReads=0.913 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:10,11:0.524:21:4,9:6,2:48:55,0,50:5.0000e+01,6.5768e-05,5.2887e+01:0.00,5.00,8.00:3,7,6,5:5,5,6,5 +17 41275645 . A G 50.00 . AC=1;AF=0.500;AN=2;DP=32;FS=1.406;MQ=237.21;MQRankSum=-1.397;QD=1.56;ReadPosRankSum=2.152;SOR=0.986;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:15,17:0.531:32:11,9:4,8:48:85,0,50:5.0000e+01,6.6587e-05,5.2731e+01:0.00,34.77,37.77:7,8,10,7:7,8,8,9 +17 41276247 . A G 44.97 . AC=1;AF=0.500;AN=2;DP=29;FS=1.562;MQ=250.00;MQRankSum=4.291;QD=1.55;ReadPosRankSum=1.990;SOR=0.368;FractionInformativeReads=0.966 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:18,10:0.357:28:9,6:9,4:44:80,0,50:4.4969e+01,1.6008e-04,5.3000e+01:0.00,34.77,37.77:11,7,5,5:12,6,5,5 +17 41276348 . T C 48.84 . AC=1;AF=0.500;AN=2;DP=31;FS=0.000;MQ=240.33;MQRankSum=1.004;QD=1.58;ReadPosRankSum=0.711;SOR=0.750;FractionInformativeReads=0.968 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:17,13:0.433:30:9,6:8,7:47:84,0,50:4.8837e+01,7.8526e-05,5.3000e+01:0.00,34.77,37.77:9,8,6,7:11,6,5,8 +17 41277187 . G C 50.00 . AC=1;AF=0.500;AN=2;DP=28;FS=1.527;MQ=250.00;MQRankSum=4.480;QD=1.79;ReadPosRankSum=1.585;SOR=0.307;FractionInformativeReads=1.000 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB 0/1:14,14:0.500:28:6,6:8,8:48:85,0,50:5.0000e+01,6.5195e-05,5.3000e+01:0.00,34.77,37.77:5,9,7,7:7,7,9,5 +MT 152 . T C . . DP=10588;MQ=246.58;FractionInformativeReads=1.000 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 1/1:98.13:2,10582:1.000:2,5156:0,5426:10584:0,2,5059,5523:0,2,5167,5415 +MT 263 . A G . . DP=7642;MQ=246.40;FractionInformativeReads=0.998 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 1/1:98.13:0,7628:1.000:0,3405:0,4223:7628:0,0,2041,5587:0,0,3626,4002 +MT 302 . A AC . . DP=4218;MQ=247.67;FractionInformativeReads=0.838 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 1/1:96.52:40,3496:0.989:21,1608:19,1888:3536:2,38,44,3452:17,23,1862,1634 +MT 310 . T TC . . DP=4175;MQ=246.78;FractionInformativeReads=0.896 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 1/1:96.88:7,3642:0.973:4,1610:3,2032:3742:0,7,58,3677:3,4,2056,1679 +MT 310 . T C . . DP=4175;MQ=246.78;FractionInformativeReads=0.896 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.54:7,93:0.025:4,37:3,56:3742:0,7,58,3677:3,4,2056,1679 +MT 539 . T A . . DP=6473;MQ=235.51;FractionInformativeReads=0.989 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.53:6115,290:0.045:2525,130:3590,160:6405:2370,3745,289,1:3424,2691,129,161 +MT 596 . T A . . DP=7892;MQ=207.77;FractionInformativeReads=0.995 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:17.66:7690,160:0.020:3512,99:4178,61:7850:3707,3983,157,3:4085,3605,96,64 +MT 605 . T A . . DP=6076;MQ=204.20;FractionInformativeReads=0.997 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.53:5916,142:0.023:2735,91:3181,51:6058:2903,3013,141,1:3146,2770,90,52 +MT 610 . T A . . DP=6178;MQ=200.16;FractionInformativeReads=0.992 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:3.40:5986,143:0.023:2788,98:3198,45:6129:2867,3119,143,0:3157,2829,98,45 +MT 616 . T A . . DP=6279;MQ=197.26;FractionInformativeReads=0.997 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:0.12:6178,83:0.013:2898,48:3280,35:6261:3085,3093,83,0:3267,2911,48,35 +MT 750 . A G . . DP=7835;MQ=167.68;FractionInformativeReads=0.998 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 1/1:98.13:1,7818:1.000:1,3815:0,4003:7819:1,0,4126,3692:1,0,3979,3839 +MT 1438 . A G . . DP=9183;MQ=112.29;FractionInformativeReads=0.999 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 1/1:98.13:2,9168:1.000:2,4631:0,4537:9170:1,1,4572,4596:1,1,4635,4533 +MT 2141 . T TAG . . DP=6592;MQ=154.12;FractionInformativeReads=0.954 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:20.00:6260,26:0.004:3130,12:3130,14:6286:3177,3083,7,19:3153,3107,13,13 +MT 2259 . C T . . DP=7544;MQ=227.78;FractionInformativeReads=0.998 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 1/1:98.13:3,7525:1.000:2,3657:1,3868:7528:2,1,3914,3611:3,0,3786,3739 +MT 2645 . G A . . DP=9206;MQ=168.00;FractionInformativeReads=0.999 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.53:9159,34:0.004:4638,16:4521,18:9193:4508,4651,16,18:4619,4540,18,16 +MT 3572 . T G . . DP=7917;MQ=248.16;FractionInformativeReads=0.997 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.53:6937,638:0.081:2745,329:4192,309:7895:1647,5290,943,15:3297,3640,481,477 +MT 3572 . T A . . DP=7917;MQ=248.16;FractionInformativeReads=0.997 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.49:6937,320:0.041:2745,163:4192,157:7895:1647,5290,943,15:3297,3640,481,477 +MT 3577 . A C . . DP=8021;MQ=248.13;FractionInformativeReads=0.995 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.53:7519,460:0.058:3006,267:4513,193:7979:2383,5136,408,52:3530,3989,235,225 +MT 3578 . T A . . DP=8000;MQ=248.14;FractionInformativeReads=0.990 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.53:7041,569:0.072:2752,252:4289,317:7921:1914,5127,788,92:3377,3664,423,457 +MT 3578 . T G . . DP=8000;MQ=248.14;FractionInformativeReads=0.990 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.53:7041,311:0.039:2752,231:4289,80:7921:1914,5127,788,92:3377,3664,423,457 +MT 3583 . A C . . DP=8074;MQ=248.16;FractionInformativeReads=0.997 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.53:7746,303:0.038:3179,156:4567,147:8049:2599,5147,264,39:3704,4042,131,172 +MT 3590 . T A . . DP=8051;MQ=248.23;FractionInformativeReads=0.949 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.53:6859,779:0.102:2837,316:4022,463:7638:1620,5239,778,1:3372,3487,315,464 +MT 3593 . T G . . DP=8106;MQ=248.23;FractionInformativeReads=0.997 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:0.51:7844,234:0.029:3286,106:4558,128:8078:2682,5162,234,0:3784,4060,106,128 +MT 3595 . A C . . DP=8121;MQ=248.28;FractionInformativeReads=0.999 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.22:7958,153:0.019:3329,71:4629,82:8111:2867,5091,148,5:3770,4188,66,87 +MT 3599 . T A . . DP=8145;MQ=248.35;FractionInformativeReads=0.972 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.53:7408,505:0.064:3093,246:4315,259:7913:2259,5149,498,7:3682,3726,239,266 +MT 3605 . T A . . DP=5766;MQ=249.86;FractionInformativeReads=0.979 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.53:5371,274:0.049:2250,122:3121,152:5645:1539,3832,273,1:2710,2661,121,153 +MT 3614 . T A . . DP=5839;MQ=249.84;FractionInformativeReads=0.974 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:20.35:5553,136:0.024:2327,62:3226,74:5689:1830,3723,132,4:2804,2749,58,78 +MT 3631 . T A . . DP=5923;MQ=249.88;FractionInformativeReads=0.995 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:20.17:5740,153:0.026:2475,59:3265,94:5893:2116,3624,153,0:2909,2831,59,94 +MT 3633 . T A . . DP=5980;MQ=249.88;FractionInformativeReads=0.994 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:10.82:5829,114:0.019:2502,42:3327,72:5943:2216,3613,113,1:2939,2890,41,73 +MT 4434 . T G . . DP=11070;MQ=40.98;FractionInformativeReads=0.712 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:0.79:7711,167:0.021:3810,76:3901,91:7878:3632,4079,2,165:3861,3850,91,76 +MT 4491 . G A . . DP=11171;MQ=36.78;FractionInformativeReads=0.547 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:14.25:6096,12:0.002:3000,5:3096,7:6108:1723,4373,3,9:3101,2995,10,2 +MT 4745 . A G . . DP=8622;MQ=56.12;FractionInformativeReads=0.494 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB:PS 1|1:94.10:0,4255:1.000:0,2121:0,2134:4255:0,0,3449,806:0,0,2147,2108:4745 +MT 4769 . A G . . DP=7846;MQ=58.69;FractionInformativeReads=0.524 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB:PS 1|1:96.49:0,4115:1.000:0,2037:0,2078:4115:0,0,3405,710:0,0,2061,2054:4745 +MT 6518 . C T . . DP=9527;MQ=114.00;FractionInformativeReads=0.998 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.40:9464,40:0.004:4669,16:4795,24:9504:4740,4724,18,22:4769,4695,18,22 +MT 7337 . G A . . DP=10647;MQ=52.11;FractionInformativeReads=0.832 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 1/1:93.49:2,8853:1.000:1,4308:1,4545:8855:1,1,4020,4833:2,0,4443,4410 +MT 8129 . A C . . DP=8194;MQ=123.14;FractionInformativeReads=0.997 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:20.26:7971,202:0.025:4011,81:3960,121:8173:4635,3336,0,202:3975,3996,121,81 +MT 8860 . A G . . DP=7566;MQ=38.95;FractionInformativeReads=0.659 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 1/1:91.87:0,4988:1.000:0,2331:0,2657:4988:0,0,1956,3032:0,0,2575,2413 +MT 13326 . T C . . DP=9172;MQ=137.21;FractionInformativeReads=0.999 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 1/1:98.13:2,9161:1.000:1,4513:1,4648:9163:1,1,4499,4662:0,2,4587,4574 +MT 13680 . C T . . DP=5597;MQ=223.37;FractionInformativeReads=0.997 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 1/1:98.13:1,5556:0.996:0,2427:1,3129:5581:1,0,2185,3395:0,1,2702,2878 +MT 13680 . C G . . DP=5597;MQ=223.37;FractionInformativeReads=0.997 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:25.75:1,24:0.004:0,18:1,6:5581:1,0,2185,3395:0,1,2702,2878 +MT 13752 . T G . . DP=4794;MQ=249.72;FractionInformativeReads=0.997 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.51:4714,65:0.014:1891,35:2823,30:4779:1247,3467,34,31:2396,2318,18,47 +MT 13762 . T G . . DP=4708;MQ=249.81;FractionInformativeReads=0.996 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.53:4509,180:0.038:1799,68:2710,112:4689:992,3517,175,5:2362,2147,63,117 +MT 13768 . T G . . DP=4797;MQ=249.81;FractionInformativeReads=0.996 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.53:4623,155:0.032:1875,39:2748,116:4778:1117,3506,149,6:2449,2174,35,120 +MT 13769 . T G . . DP=4818;MQ=249.81;FractionInformativeReads=0.996 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.53:4684,115:0.024:1911,20:2773,95:4799:1146,3538,113,2:2471,2213,20,95 +MT 14831 . G A . . DP=8865;MQ=207.09;FractionInformativeReads=0.998 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 1/1:98.13:3,8829:0.998:2,4182:1,4647:8846:3,0,4595,4248:2,1,4535,4308 +MT 14831 . G C . . DP=8865;MQ=207.09;FractionInformativeReads=0.998 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:49.84:3,14:0.002:2,11:1,3:8846:3,0,4595,4248:2,1,4535,4308 +MT 14872 . C T . . DP=6672;MQ=204.38;FractionInformativeReads=0.999 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 1/1:98.13:5,6662:0.999:3,3178:2,3484:6667:4,1,3354,3308:4,1,3346,3316 +MT 14918 . G A . . DP=6809;MQ=194.78;FractionInformativeReads=1.000 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:21.37:6570,237:0.035:3161,125:3409,112:6807:3373,3197,121,116:3320,3250,123,114 +MT 15326 . A G . . DP=7656;MQ=235.28;FractionInformativeReads=0.999 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 1/1:98.13:1,7647:1.000:1,3755:0,3892:7648:1,0,3740,3907:1,0,3774,3873 +MT 16023 . G A . . DP=9292;MQ=249.42;FractionInformativeReads=0.998 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 0/1:51.92:2572,6705:0.723:1247,3381:1325,3324:9277:1271,1301,3404,3301:1288,1284,3412,3293 diff --git a/tests/seqvars/ingest/NA12878_dragen.vcf.gz b/tests/seqvars/ingest/NA12878_dragen.vcf.gz new file mode 100644 index 00000000..790d8fe6 Binary files /dev/null and b/tests/seqvars/ingest/NA12878_dragen.vcf.gz differ diff --git a/tests/seqvars/ingest/NA12878_dragen.vcf.gz.tbi b/tests/seqvars/ingest/NA12878_dragen.vcf.gz.tbi new file mode 100644 index 00000000..67cfae88 Binary files /dev/null and b/tests/seqvars/ingest/NA12878_dragen.vcf.gz.tbi differ diff --git a/tests/seqvars/ingest/db/bootstrap.sh b/tests/seqvars/ingest/db/bootstrap.sh new file mode 100644 index 00000000..4b8583cf --- /dev/null +++ b/tests/seqvars/ingest/db/bootstrap.sh @@ -0,0 +1,55 @@ +#!/usr/bin/bash + +# Helper script that bootstraps the database for the tests. +# +# We include transcripts, clinvar, and frequencies for BRCA1 only. + +set -x + +SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd ) + +mkdir -p $SCRIPT_DIR/{grch37,grch38} + +# transcripts + +wget -O /tmp/cdot-0.2.12.refseq.grch37_grch38.json.gz \ + https://github.com/SACGF/cdot/releases/download/v0.2.12/cdot-0.2.12.refseq.grch37_grch38.json.gz + +mehari \ + db \ + create \ + txs \ + --path-out \ + $SCRIPT_DIR/grch37/txs.bin.zst \ + --path-cdot-json \ + /tmp/cdot-0.2.12.refseq.grch37_grch38.json.gz \ + --path-seqrepo-instance \ + ~/Data/mehari/db-workspace/b37/seqrepo-data/master \ + --genome-release \ + grch37 \ + --gene-symbols BRCA1 + +# clinvar + +wget -O /tmp/annonars-clinvar-minimal-grch37-20230910+0.18.0.tar.gz \ + https://github.com/bihealth/annonars-data-clinvar/releases/download/clinvar-weekly-20230910/annonars-clinvar-minimal-grch37-20230910+0.18.0.tar.gz +tar --strip-components 2 -C /tmp -xvf /tmp/annonars-clinvar-minimal-grch37-20230910+0.18.0.tar.gz + +mkdir -p $SCRIPT_DIR/grch37/seqvars/clinvar +cp /tmp/annonars-clinvar-minimal-grch37-20230910+0.18.0/spec.yaml \ + $SCRIPT_DIR/grch37/seqvars/clinvar +annonars db-utils copy \ + --path-in /tmp/annonars-clinvar-minimal-grch37-20230910+0.18.0/rocksdb \ + --path-out $SCRIPT_DIR/grch37/seqvars/clinvar/rocksdb \ + --range 17:41183866:41337086 + +# frequencies + +DOWNLOADER=/data/sshfs/data/cephfs-1/work/projects/cubi_varfish_data/2023-06-05_varfish-db-downloader/varfish-db-downloader +mkdir -p mkdir -p $SCRIPT_DIR/grch37/seqvars/freqs +cp $DOWNLOADER/output/full/mehari/freqs-grch37-2.1.1+2.1.1+3.1+20200327+0.19.0/spec.yaml \ + $SCRIPT_DIR/grch37/seqvars/freqs +annonars db-utils copy \ + --path-in $DOWNLOADER/output/full/mehari/freqs-grch37-2.1.1+2.1.1+3.1+20200327+0.19.0/rocksdb \ + --path-out $SCRIPT_DIR/grch37/seqvars/freqs/rocksdb \ + --range 17:41183866:41337086 diff --git a/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/000014.sst b/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/000014.sst new file mode 100644 index 00000000..77518c5d --- /dev/null +++ b/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/000014.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:c7f8fc20cf124045d5fdf0050e4af94358f2b25d1b310b205370d5d4dbcc7a50 +size 1343 diff --git a/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/000016.sst b/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/000016.sst new file mode 100644 index 00000000..89048f37 --- /dev/null +++ b/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/000016.sst @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:9735dbd544395502b1ec1a082c7cbfb4abac8e74f23190fc9340ad007d5f1835 +size 248747 diff --git a/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/CURRENT b/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/CURRENT new file mode 100644 index 00000000..f8d50486 --- /dev/null +++ b/tests/seqvars/ingest/db/grch37/seqvars/clinvar/rocksdb/CURRENT @@ -0,0 +1,3 @@ +version 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