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/mod.rs b/src/seqvars/ingest/mod.rs new file mode 100644 index 00000000..e4773249 --- /dev/null +++ b/src/seqvars/ingest/mod.rs @@ -0,0 +1,71 @@ +//! Implementation of `seqvars ingest` subcommand. + +use crate::common::{self, GenomeRelease}; + +/// 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 { + /// The assumed genome build. + #[clap(long)] + pub genomebuild: GenomeRelease, + /// Path to input file. + #[clap(long)] + pub path_in: String, + /// Path to output file. + #[clap(long)] + pub path_out: String, +} + +/// 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!( + "All of `seqvars ingest` completed in {:?}", + before_anything.elapsed() + ); + Ok(()) +} + +#[cfg(test)] +mod test { + 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")] + fn smoke_test_run(#[case] path: &str) { + set_snapshot_suffix!("{:?}", path.split('/').last().unwrap().replace(".", "_")); + + let tmpdir = temp_testdir::TempDir::default(); + + let args_common = Default::default(); + let args = super::Args { + genomebuild: GenomeRelease::Grch37, + path_in: path.into(), + path_out: tmpdir + .join("out.vcf") + .to_str() + .expect("invalid path") + .into(), + }; + super::run(&args_common, &args).unwrap(); + } +} diff --git a/src/seqvars/mod.rs b/src/seqvars/mod.rs new file mode 100644 index 00000000..b3ac910a --- /dev/null +++ b/src/seqvars/mod.rs @@ -0,0 +1 @@ +pub mod ingest; diff --git a/tests/seqvars/ingest/example_dragen.07.021.624.3.10.4.vcf b/tests/seqvars/ingest/example_dragen.07.021.624.3.10.4.vcf new file mode 100644 index 00000000..91cd29a7 --- /dev/null +++ b/tests/seqvars/ingest/example_dragen.07.021.624.3.10.4.vcf @@ -0,0 +1,120 @@ +##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 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 +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 diff --git a/tests/seqvars/ingest/example_dragen_chrmt.vcf b/tests/seqvars/ingest/example_dragen.07.021.624.3.10.9.vcf similarity index 73% rename from tests/seqvars/ingest/example_dragen_chrmt.vcf rename to tests/seqvars/ingest/example_dragen.07.021.624.3.10.9.vcf index 8159958d..329baacb 100644 --- a/tests/seqvars/ingest/example_dragen_chrmt.vcf +++ b/tests/seqvars/ingest/example_dragen.07.021.624.3.10.9.vcf @@ -1,41 +1,38 @@ ##fileformat=VCFv4.2 -##FILTER= ##FORMAT= ##FORMAT= ##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= ##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= ##INFO= +##INFO= +##INFO= +##INFO= ##FILTER= ##FILTER= ##FILTER= -##FILTER= -##FILTER= ##FILTER= -##FILTER= +##FILTER= ##FILTER= ##FILTER= ##FILTER= @@ -140,5 +137,6 @@ ##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 INDEX PARENT_B PARENT_A -MT 73 . A G . PASS DP=7407;MQ=229.88 GT:AD:AF:DP:FT:SQ:F1R2:F2R1 0/0:2831,6:0.002:1919:PASS:99:.:. 1/1:0,2032:1:2032:PASS:98.13:0,921:0,1111 0/0:4731,17:0.004:3115:PASS:99:.:. +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CASE +17 41256074 . CA C 49.57 PASS AC=1;AF=0.500;AN=2;DP=40;FS=1.397;MQ=249.24;MQRankSum=4.084;QD=1.24;ReadPosRankSum=1.804;SOR=1.051;FractionInformativeReads=0.800 GT:AD:AF:DP:F1R2:F2R1:GQ:PL:GP:PRI:SB:MB:PS 0|1:18,14:0.438:32:9,10:9,4:47:60,0,47:4.9567e+01,9.1418e-05,5.0000e+01:0.00,10.00,13.01:10,8,9,5:9,9,9,5:41256074 +MT 750 . A G . PASS DP=5639;MQ=150.72;FractionInformativeReads=0.995 GT:SQ:AD:AF:F1R2:F2R1:DP:SB:MB 1/1:98.13:1,5607:1.000:0,2721:1,2886:5608:0,1,3291,2316:1,0,2879,2728 diff --git a/tests/seqvars/ingest/example_gatk_hc.vcf b/tests/seqvars/ingest/example_gatk_hc.3.7-0.vcf similarity index 53% rename from tests/seqvars/ingest/example_gatk_hc.vcf rename to tests/seqvars/ingest/example_gatk_hc.3.7-0.vcf index 9a7cdb21..efb63e80 100644 --- a/tests/seqvars/ingest/example_gatk_hc.vcf +++ b/tests/seqvars/ingest/example_gatk_hc.3.7-0.vcf @@ -122,113 +122,5 @@ ##bcftools_concatVersion=1.12+htslib-1.12 ##bcftools_concatCommand=concat --allow-overlaps -d none -o output/out.vcf.gz -O z job_out.0.d/out/tmp_0.vcf.gz job_out.1.d/out/tmp_1.vcf.gz job_out.2.d/out/tmp_2.vcf.gz job_out.3.d/out/tmp_3.vcf.gz job_out.4.d/out/tmp_4.vcf.gz job_out.5.d/out/tmp_5.vcf.gz job_out.6.d/out/tmp_6.vcf.gz job_out.7.d/out/tmp_7.vcf.gz job_out.8.d/out/tmp_8.vcf.gz job_out.9.d/out/tmp_9.vcf.gz job_out.10.d/out/tmp_10.vcf.gz 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job_out.616.d/out/tmp_616.vcf.gz job_out.617.d/out/tmp_617.vcf.gz job_out.618.d/out/tmp_618.vcf.gz job_out.619.d/out/tmp_619.vcf.gz job_out.620.d/out/tmp_620.vcf.gz job_out.621.d/out/tmp_621.vcf.gz job_out.622.d/out/tmp_622.vcf.gz job_out.623.d/out/tmp_623.vcf.gz job_out.624.d/out/tmp_624.vcf.gz job_out.625.d/out/tmp_625.vcf.gz job_out.626.d/out/tmp_626.vcf.gz job_out.627.d/out/tmp_627.vcf.gz job_out.628.d/out/tmp_628.vcf.gz job_out.629.d/out/tmp_629.vcf.gz job_out.630.d/out/tmp_630.vcf.gz job_out.631.d/out/tmp_631.vcf.gz job_out.632.d/out/tmp_632.vcf.gz job_out.633.d/out/tmp_633.vcf.gz job_out.634.d/out/tmp_634.vcf.gz job_out.635.d/out/tmp_635.vcf.gz job_out.636.d/out/tmp_636.vcf.gz job_out.637.d/out/tmp_637.vcf.gz job_out.638.d/out/tmp_638.vcf.gz job_out.639.d/out/tmp_639.vcf.gz job_out.640.d/out/tmp_640.vcf.gz job_out.641.d/out/tmp_641.vcf.gz job_out.642.d/out/tmp_642.vcf.gz job_out.643.d/out/tmp_643.vcf.gz job_out.644.d/out/tmp_644.vcf.gz job_out.645.d/out/tmp_645.vcf.gz job_out.646.d/out/tmp_646.vcf.gz job_out.647.d/out/tmp_647.vcf.gz job_out.648.d/out/tmp_648.vcf.gz job_out.649.d/out/tmp_649.vcf.gz job_out.650.d/out/tmp_650.vcf.gz job_out.651.d/out/tmp_651.vcf.gz job_out.652.d/out/tmp_652.vcf.gz job_out.653.d/out/tmp_653.vcf.gz job_out.654.d/out/tmp_654.vcf.gz job_out.655.d/out/tmp_655.vcf.gz job_out.656.d/out/tmp_656.vcf.gz job_out.657.d/out/tmp_657.vcf.gz job_out.658.d/out/tmp_658.vcf.gz job_out.659.d/out/tmp_659.vcf.gz job_out.660.d/out/tmp_660.vcf.gz job_out.661.d/out/tmp_661.vcf.gz job_out.662.d/out/tmp_662.vcf.gz job_out.663.d/out/tmp_663.vcf.gz job_out.664.d/out/tmp_664.vcf.gz job_out.665.d/out/tmp_665.vcf.gz job_out.666.d/out/tmp_666.vcf.gz job_out.667.d/out/tmp_667.vcf.gz job_out.668.d/out/tmp_668.vcf.gz job_out.669.d/out/tmp_669.vcf.gz job_out.670.d/out/tmp_670.vcf.gz job_out.671.d/out/tmp_671.vcf.gz 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 41190140 rs34738736 A AAC 1546.86 . AC=3;AF=0.5;AN=6;BaseQRankSum=-1.671;ClippingRankSum=0;DB;DP=125;ExcessHet=1.549;FS=1.566;MLEAC=3;MLEAF=0.5;MQ=60;MQRankSum=0;QD=22.42;ReadPosRankSum=-0.91;SOR=0.624 GT:AD:DP:GQ:PL 1/1:0,39:39:99:1248,120,0 0/1:16,14:30:99:344,0,411 0/0:33,0:33:99:0,100,1042 -17 41197784 rs41293465 G A 1024.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=1.294;ClippingRankSum=0;DB;DP=103;ExcessHet=3.9794;FS=3.902;MLEAC=2;MLEAF=0.333;MQ=60;MQRankSum=0;QD=15.76;ReadPosRankSum=0.499;SOR=1.169 GT:AD:DP:GQ:PL 0/0:38,0:38:99:0,114,1309 0/1:10,16:26:99:478,0,279 0/1:19,20:39:99:578,0,543 -17 41199002 rs8176313 C T 584.13 . AC=1;AF=0.167;AN=6;BaseQRankSum=-0.198;ClippingRankSum=0;DB;DP=136;ExcessHet=3.0103;FS=3.013;MLEAC=1;MLEAF=0.167;MQ=60;MQRankSum=0;QD=12.98;ReadPosRankSum=-1.018;SOR=0.59 GT:AD:DP:GQ:PL 0/1:22,23:45:99:615,0,620 0/0:39,0:39:99:0,117,1301 0/0:50,0:50:99:0,150,1698 -17 41204797 rs562562021 A AAC 447.12 . AC=2;AF=0.333;AN=6;BaseQRankSum=1.369;ClippingRankSum=0;DB;DP=95;ExcessHet=3.9794;FS=1.061;MLEAC=2;MLEAF=0.333;MQ=60;MQRankSum=0;QD=10.65;ReadPosRankSum=1.522;SOR=0.882 GT:AD:DP:GQ:PL 0/0:20,0:20:61:0,61,741 0/1:7,9:16:99:216,0,265 0/1:13,13:26:99:272,0,508 -17 41204834 rs761604604 ACACACACT A 467.09 . AC=1;AF=0.167;AN=6;BaseQRankSum=-1.241;ClippingRankSum=0;DB;DP=90;ExcessHet=3.0103;FS=6.894;MLEAC=1;MLEAF=0.167;MQ=60;MQRankSum=0;QD=17.97;ReadPosRankSum=1.943;SOR=0.442 GT:AD:DP:GQ:PL 0/0:22,0:22:65:0,65,988 0/0:20,0:20:60:0,60,860 0/1:13,13:26:99:507,0,506 -17 41204840 rs781493445 ACT A 340.12 . AC=2;AF=0.333;AN=6;BaseQRankSum=-3.187;ClippingRankSum=0;DB;DP=86;ExcessHet=3.9794;FS=2.485;MLEAC=2;MLEAF=0.333;MQ=60;MQRankSum=0;QD=9.45;ReadPosRankSum=1.28;SOR=0.354 GT:AD:DP:GQ:PL 0/1:8,11:19:99:242,0,162 0/1:10,7:17:99:139,0,399 0/0:26,0:26:79:0,79,1171 -17 41204842 rs9897397 T A 732.92 . AC=3;AF=0.5;AN=6;BaseQRankSum=0;ClippingRankSum=0;DB;DP=86;ExcessHet=6.9897;FS=7.31;MLEAC=3;MLEAF=0.5;MQ=60;MQRankSum=0;QD=12.02;ReadPosRankSum=-1.221;SOR=1.744 GT:AD:DP:GQ:PL 0/1:12,8:20:99:157,0,263 0/1:7,10:17:99:296,0,140 0/1:13,11:24:99:310,0,513 -17 41204856 rs17671533 G A 1274.9 . AC=3;AF=0.5;AN=6;BaseQRankSum=0.447;ClippingRankSum=0;DB;DP=88;ExcessHet=1.549;FS=5.934;MLEAC=3;MLEAF=0.5;MQ=60;MQRankSum=0;QD=22.77;ReadPosRankSum=0.786;SOR=1.453 GT:AD:DP:GQ:PL 1/1:0,33:33:98:1087,98,0 0/1:14,9:23:99:224,0,383 0/0:31,0:31:93:0,93,1028 17 41210126 rs542522579 C CTAGCACTT 1136.12 . AC=2;AF=0.333;AN=6;BaseQRankSum=-1.948;ClippingRankSum=0;DB;DP=98;ExcessHet=3.9794;FS=0.876;MLEAC=2;MLEAF=0.333;MQ=60;MQRankSum=0;QD=16.71;ReadPosRankSum=-1.999;SOR=0.527 GT:AD:DP:GQ:PL 0/0:29,0:29:87:0,87,2916 0/1:23,13:36:99:466,0,2205 0/1:15,17:32:99:711,0,1410 -17 41213748 rs8176267 T C 2167.9 . AC=3;AF=0.5;AN=6;BaseQRankSum=-1.332;ClippingRankSum=0;DB;DP=128;ExcessHet=1.549;FS=2.252;MLEAC=3;MLEAF=0.5;MQ=60;MQRankSum=0;QD=26.44;ReadPosRankSum=-0.058;SOR=0.674 GT:AD:DP:GQ:PL 1/1:0,48:48:99:1656,144,0 0/1:15,19:34:99:548,0,419 0/0:45,0:45:99:0,135,1564 -17 41216844 rs759922390 A AT 107.09 . AC=1;AF=0.167;AN=6;BaseQRankSum=-0.292;ClippingRankSum=0;DB;DP=85;ExcessHet=3.0103;FS=0;MLEAC=1;MLEAF=0.167;MQ=60;MQRankSum=0;QD=5.95;ReadPosRankSum=-0.968;SOR=0.673 GT:AD:DP:GQ:PL 0/0:19,0:19:57:0,57,384 0/0:17,1:18:35:0,35,325 0/1:8,10:18:99:147,0,107 -17 41219907 rs772731581 T TA 594.88 . AC=6;AF=1;AN=6;BaseQRankSum=-0.337;ClippingRankSum=0;DB;DP=47;ExcessHet=3.0103;FS=0;MLEAC=6;MLEAF=1;MQ=60;MQRankSum=0;QD=18.03;ReadPosRankSum=0.578;SOR=0.412 GT:AD:DP:GQ:PL 1/1:0,12:12:36:239,36,0 1/1:0,9:9:27:179,27,0 1/1:1,11:12:20:212,20,0 -17 41224892 rs533819030 G GT 1094.86 . AC=3;AF=0.5;AN=6;BaseQRankSum=-0.974;ClippingRankSum=0;DB;DP=122;ExcessHet=1.549;FS=0.793;MLEAC=3;MLEAF=0.5;MQ=60;MQRankSum=0;QD=15.87;ReadPosRankSum=-0.934;SOR=0.878 GT:AD:DP:GQ:PL 1/1:0,33:33:98:833,98,0 0/1:19,17:36:99:307,0,356 0/0:31,0:31:93:0,93,758 -17 41225176 rs148436838 C T 1453.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=1.917;ClippingRankSum=0;DB;DP=139;ExcessHet=3.9794;FS=4.187;MLEAC=2;MLEAF=0.333;MQ=60;MQRankSum=0;QD=15.14;ReadPosRankSum=0.063;SOR=1.049 GT:AD:DP:GQ:PL 0/0:42,0:42:99:0,126,1440 0/1:23,24:47:99:693,0,626 0/1:22,27:49:99:792,0,593 -17 41229777 rs11368665 G GT 3992.86 . AC=6;AF=1;AN=6;DB;DP=122;ExcessHet=3.0103;FS=0;MLEAC=6;MLEAF=1;MQ=59.93;QD=33.55;SOR=1.297 GT:AD:DP:GQ:PL 1/1:0,44:44:99:1476,132,0 1/1:0,33:33:99:1110,99,0 1/1:0,42:42:99:1442,129,0 -17 41232344 rs6416927 G C 3635.9 . AC=6;AF=1;AN=6;DB;DP=107;ExcessHet=3.0103;FS=0;MLEAC=6;MLEAF=1;MQ=60;QD=33.98;SOR=0.75 GT:AD:DP:GQ:PL 1/1:0,32:32:96:1077,96,0 1/1:0,32:32:96:1110,96,0 1/1:0,43:43:99:1475,129,0 -17 41238126 rs60834728 T TAC 265.09 . AC=1;AF=0.167;AN=6;BaseQRankSum=-2.133;ClippingRankSum=0;DB;DP=101;ExcessHet=3.0103;FS=4.217;MLEAC=1;MLEAF=0.167;MQ=60;MQRankSum=0;QD=9.82;ReadPosRankSum=0.069;SOR=0.779 GT:AD:DP:GQ:PL 0/0:26,0:26:78:0,78,723 0/0:28,0:28:84:0,84,783 0/1:13,14:27:99:305,0,281 -17 41238969 rs150347361 G C 460.13 . AC=1;AF=0.167;AN=6;BaseQRankSum=-0.255;ClippingRankSum=0;DB;DP=108;ExcessHet=3.0103;FS=7.156;MLEAC=1;MLEAF=0.167;MQ=60;MQRankSum=0;QD=15.34;ReadPosRankSum=1.315;SOR=1.302 GT:AD:DP:GQ:PL 0/0:43,0:43:99:0,129,1475 0/0:35,0:35:99:0,105,1197 0/1:13,17:30:99:491,0,362 -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 rs10445302 T A 144.16 . AC=2;AF=0.333;AN=6;BaseQRankSum=-1.316;ClippingRankSum=0;DB;DP=56;ExcessHet=3.9794;FS=6.692;MLEAC=2;MLEAF=0.333;MQ=60;MQRankSum=0;QD=6.27;ReadPosRankSum=0.392;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 41254393 . G T 37.68 . AC=1;AF=0.167;AN=6;BaseQRankSum=-3.039;ClippingRankSum=0;DP=89;ExcessHet=3.6798;FS=38.246;MLEAC=1;MLEAF=0.167;MQ=60;MQRankSum=0;QD=1.02;ReadPosRankSum=2.515;SOR=5.282 GT:AD:DP:GQ:PL 0/1:29,8:37:66:66,0,688 ./.:.:.:.:. 0/0:32,3:35:47:0,47,877 -17 41273700 . C CA 43.64 . AC=1;AF=0.167;AN=6;BaseQRankSum=0.99;ClippingRankSum=0;DP=49;ExcessHet=3.0103;FS=2.548;MLEAC=1;MLEAF=0.167;MQ=60;MQRankSum=0;QD=4.36;ReadPosRankSum=0.975;SOR=1.371 GT:AD:DP:GQ:PL 0/0:14,0:14:42:0,42,274 0/0:6,1:7:10:0,10,104 0/1:5,5:10:65:81,0,65 -17 41280040 rs61243891 CA C 99.22 . AC=2;AF=0.333;AN=6;BaseQRankSum=-0.395;ClippingRankSum=0;DB;DP=47;ExcessHet=3.9794;FS=8.659;MLEAC=2;MLEAF=0.333;MQ=60;MQRankSum=0;QD=4.13;ReadPosRankSum=-0.099;SOR=0.674 GT:AD:DP:GQ:PL 0/0:6,0:6:18:0,18,115 0/1:5,5:10:57:57,0,67 0/1:7,7:14:83:83,0,85 -17 41294957 . GTATATATATA G 1218.12 . AC=2;AF=0.333;AN=6;BaseQRankSum=1.666;ClippingRankSum=0;DP=119;ExcessHet=3.9794;FS=2.878;MLEAC=2;MLEAF=0.333;MQ=60;MQRankSum=0;QD=16.24;ReadPosRankSum=-1.276;SOR=1.085 GT:AD:DP:GQ:PL 0/0:43,0:43:99:0,129,8633 0/1:16,16:32:99:589,0,3717 0/1:23,20:43:99:670,0,5223 -17 41294969 . GTGTGTGTGTGTGTGTA G 1198.12 . AC=2;AF=0.333;AN=6;BaseQRankSum=2.117;ClippingRankSum=0;DP=132;ExcessHet=3.9794;FS=2.799;MLEAC=2;MLEAF=0.333;MQ=60;MQRankSum=0;QD=14.61;ReadPosRankSum=0.406;SOR=1.045 GT:AD:DP:GQ:PL 0/0:50,0:50:99:0,150,8872 0/1:20,16:36:99:577,0,3838 0/1:26,20:46:99:662,0,5313 -17 41307485 rs9903972 A C 4132.9 . 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