diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsEngine.java index bf263afdebc..1cf1e344cc0 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsEngine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsEngine.java @@ -470,16 +470,21 @@ static List cleanupGenotypeAnnotations(final VariantContext vc, final } if ( createRefGTs ) { - // move the GQ to RGQ - if (oldGT.hasGQ()) { + //keep 0 depth samples and 0 GQ samples as no-call + if (depth > 0 && oldGT.hasGQ()) { + if (oldGT.getGQ() > 0) { + final List refAlleles = Collections.nCopies(oldGT.getPloidy(), vc.getReference()); + builder.alleles(refAlleles); + } else { + builder.alleles(Collections.nCopies(oldGT.getPloidy(),Allele.NO_CALL)); + } + + // move the GQ to RGQ builder.noGQ(); attrs.put(GATKVCFConstants.REFERENCE_GENOTYPE_QUALITY, oldGT.getGQ()); - } - - //keep 0 depth samples and 0 GQ samples as no-call - if (depth > 0 && oldGT.hasGQ() && oldGT.getGQ() > 0) { - final List refAlleles = Collections.nCopies(oldGT.getPloidy(), vc.getReference()); - builder.alleles(refAlleles); + } else { + builder.alleles(Collections.nCopies(oldGT.getPloidy(),Allele.NO_CALL)); + builder.noGQ().noDP(); } // also, the PLs are technically no longer usable diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/gnarlyGenotyper/GnarlyGenotyperEngine.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/gnarlyGenotyper/GnarlyGenotyperEngine.java index b53d04f76f7..9b6c5030497 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/gnarlyGenotyper/GnarlyGenotyperEngine.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/gnarlyGenotyper/GnarlyGenotyperEngine.java @@ -393,14 +393,8 @@ protected GenotypesContext iterateOnGenotypes(final VariantContext vc, final Lis protected void makeGenotypeCall(final Genotype g, final GenotypeBuilder gb, final double[] genotypeLikelihoods, final List allelesToUse) { - if ( genotypeLikelihoods == null || !GATKVariantContextUtils.isInformative(genotypeLikelihoods) ) { - //gb.alleles(GATKVariantContextUtils.noCallAlleles(g.getAlleles().size())).noGQ(); - GATKVariantContextUtils.makeGenotypeCall(g.getPloidy(), gb, GenotypeAssignmentMethod.SET_TO_NO_CALL, + GATKVariantContextUtils.makeGenotypeCall(g.getPloidy(), gb, GenotypeAssignmentMethod.USE_PLS_TO_ASSIGN, genotypeLikelihoods, allelesToUse, g, null); - } else { - GATKVariantContextUtils.makeGenotypeCall(g.getPloidy(), gb, GenotypeAssignmentMethod.USE_PLS_TO_ASSIGN, - genotypeLikelihoods, allelesToUse, g, null); - } } /** diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java index 4de6ec161b1..01822b26db8 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFsIntegrationTest.java @@ -80,7 +80,6 @@ public class GenotypeGVCFsIntegrationTest extends CommandLineProgramTest { @DataProvider(name = "gvcfsToGenotype") public Object[][] gvcfsToGenotype() { return new Object[][]{ -/* //combine not supported yet, see https://github.com/broadinstitute/gatk/issues/2429 and https://github.com/broadinstitute/gatk/issues/2584 //{"combine.single.sample.pipeline.1.vcf", null, Arrays.asList("-V", getTestFile("combine.single.sample.pipeline.2.vcf").toString() , "-V", getTestFile("combine.single.sample.pipeline.3.vcf").toString()), b37_reference_20_21}, @@ -151,7 +150,7 @@ public Object[][] gvcfsToGenotype() { getTestFile( "expected/includeLowQualSites.vcf"), Arrays.asList( " --" + GenotypeGVCFs.ALL_SITES_LONG_NAME + " -L 20:10,012,730-10,012,740"), b37_reference_20_21}, -*/ + //23 highly multi-allelic sites across 54 1000G exomes to test allele subsetting and QUAL calculation //plus one 10-allele WGS variant that's all hom-ref with one GT that has unnormalized PLs from some sort of GenomicsDB corner case //this VCF still has the haploid-looking GDB no-calls as in sample NA21137 at position chr1:3836468 -- allegedly GATK 4.2.5.0 from February 7, 2022, possibly due to --call-genotypes diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java index eef0d6158af..6df481c7322 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java @@ -1,24 +1,17 @@ package org.broadinstitute.hellbender.tools.walkers.variantutils; import htsjdk.samtools.util.BlockCompressedInputStream; -import htsjdk.variant.variantcontext.VariantContext; import org.broadinstitute.hellbender.CommandLineProgramTest; import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; import org.broadinstitute.hellbender.exceptions.UserException; import org.broadinstitute.hellbender.testutils.ArgumentsBuilder; import org.broadinstitute.hellbender.testutils.IntegrationTestSpec; -import org.broadinstitute.hellbender.testutils.VariantContextTestUtils; -import org.broadinstitute.hellbender.tools.walkers.annotator.RMSMappingQuality; -import org.broadinstitute.hellbender.utils.Utils; import org.testng.Assert; import org.testng.annotations.DataProvider; import org.testng.annotations.Test; import java.io.*; import java.util.Collections; -import java.util.List; - -import static org.broadinstitute.hellbender.testutils.VariantContextTestUtils.assertForEachElementInLists; public final class CalculateGenotypePosteriorsIntegrationTest extends CommandLineProgramTest { @@ -66,25 +59,15 @@ public void testNumRefWithPanel() throws IOException { //use the first 20 variants to save time; they have a nice range of AC from 4 to over 4000 //three variants have GTs with zero depth and PLs=[1,0,0], which should get PPs public void testUsingDiscoveredAF() throws IOException { - final File output = createTempFile("cgp_output", ".vcf"); - final ArgumentsBuilder args = new ArgumentsBuilder(); - args.addReference(new File(b37_reference_20_21)) //note we need a ref for -L arg - .add("V", largeDir + "1000G.phase3.broad.withGenotypes.chr20.10100000.vcf") - .add("L", "20:10,000,000-10,001,432") - .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, false) - .addOutput(output); - runCommandLine(args); - - Assert.assertTrue(output.exists()); - - File expected = new File(largeDir + "CalculateGenotypePosteriors/expectedCGP_testUsingDiscoveredAF.vcf"); - final List expectedVC = VariantContextTestUtils.getVariantContexts(expected); - final List actualVC = VariantContextTestUtils.getVariantContexts(output); - try { - assertForEachElementInLists(actualVC, expectedVC, VariantContextTestUtils::assertVariantContextsHaveSameGenotypes); - } catch (final AssertionError error) { - throw error; - } + final IntegrationTestSpec spec = new IntegrationTestSpec( + " -O %s" + + " -R " + b37_reference_20_21 + //NOTE: we need a reference for -L + " -L 20:10,000,000-10,001,432" + + " -V " + largeDir + "1000G.phase3.broad.withGenotypes.chr20.10100000.vcf" + + " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false", + Collections.singletonList(largeDir + "CalculateGenotypePosteriors/expectedCGP_testUsingDiscoveredAF.vcf") + ); + spec.executeTest("testUsingDiscoveredAF", this); } @Test @@ -100,28 +83,7 @@ public void testMissingPriors() throws IOException { " --" + StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE +" false", Collections.singletonList(largeDir + "CalculateGenotypePosteriors/expectedCGP_testMissingPriors.vcf") ); - //spec.executeTest("testMissingPriors", this); - - final File output = createTempFile("cgp_output", ".vcf"); - final ArgumentsBuilder args = new ArgumentsBuilder(); - args.addReference(new File(b37_reference_20_21)) //note we need a ref for -L arg - .addFlag("discovered-allele-count-priors-off") - .add("V", largeDir + "1000G.phase3.broad.withGenotypes.chr20.10100000.vcf") - .add("L", "20:10,000,000-10,001,432") - .add(StandardArgumentDefinitions.ADD_OUTPUT_VCF_COMMANDLINE, false) - .addOutput(output); - runCommandLine(args); - - Assert.assertTrue(output.exists()); - - File expected = new File(largeDir + "CalculateGenotypePosteriors/expectedCGP_testMissingPriors.vcf"); - final List expectedVC = VariantContextTestUtils.getVariantContexts(expected); - final List actualVC = VariantContextTestUtils.getVariantContexts(output); - try { - assertForEachElementInLists(actualVC, expectedVC, VariantContextTestUtils::assertVariantContextsHaveSameGenotypes); - } catch (final AssertionError error) { - throw error; - } + spec.executeTest("testMissingPriors", this); } @Test diff --git a/src/test/resources/large/gvcfs/combined.gatk3.7_30_ga4f720357.expected.vcf b/src/test/resources/large/gvcfs/combined.gatk3.7_30_ga4f720357.expected.vcf index 5d106d60ac8..d50e24418f9 100644 --- a/src/test/resources/large/gvcfs/combined.gatk3.7_30_ga4f720357.expected.vcf +++ b/src/test/resources/large/gvcfs/combined.gatk3.7_30_ga4f720357.expected.vcf @@ -3155,14 +3155,14 @@ chr20 18950504 . A C 292.29 . AC=1;AF=0.167;AN=6;BaseQRankSum=1.10;ClippingRankS chr20 18950794 . G A 274.68 . AC=2;AF=0.500;AN=4;BaseQRankSum=0.747;ClippingRankSum=1.59;DP=18;ExcessHet=1.7609;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=26.56;MQRankSum=-7.470e-01;QD=17.17;RAW_MQ=12698.00;ReadPosRankSum=1.59;SOR=2.584 GT:AD:DP:GQ:PL 0/1:1,7:8:11:178,0,11 0/1:2,6:8:46:105,0,46 ./.:2,0:2:0:0,0,10 chr20 18951454 . C T 363.16 . AC=2;AF=0.333;AN=6;DP=32;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=0.333;MQ=41.59;QD=33.01;RAW_MQ=19029.00;SOR=1.802 GT:AD:DP:GQ:PL 0/0:14,0:14:39:0,39,585 1/1:0,11:11:33:380,33,0 0/0:7,0:7:21:0,21,233 chr20 18951764 . C T 117.03 . AC=3;AF=0.500;AN=6;BaseQRankSum=-7.270e-01;ClippingRankSum=-7.270e-01;DP=9;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=0.333;MQ=23.27;MQRankSum=0.727;QD=19.51;RAW_MQ=3249.00;ReadPosRankSum=0.727;SOR=0.707 GT:AD:DP:GQ:PL 0/0:3,0:3:9:0,9,84 1/1:0,2:2:6:61,6,0 0/1:1,3:4:13:70,0,13 -chr20 18951869 . C T 91.92 . AC=2;AF=0.500;AN=4;DP=8;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=33.61;QD=22.98;RAW_MQ=4518.00;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,4:4:12:107,12,0 ./. 0/0:4,0:4:12:0,12,119 -chr20 18951894 . A T 91.92 . AC=2;AF=0.500;AN=4;DP=8;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=33.61;QD=22.98;RAW_MQ=4518.00;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,4:4:12:107,12,0 ./. 0/0:4,0:4:12:0,12,119 -chr20 18951906 . A G 36 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.736;ClippingRankSum=-7.360e-01;DP=7;ExcessHet=0.0000;FS=4.771;MLEAC=1;MLEAF=0.250;MQ=27.91;MQRankSum=-7.360e-01;QD=12.00;RAW_MQ=2337.00;ReadPosRankSum=0.736;SOR=2.225 GT:AD:DP:GQ:PL 0/0:4,0:4:12:0,12,119 ./. 0/1:1,2:3:26:44,0,26 -chr20 18951975 . G A 36.09 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.736;ClippingRankSum=-7.360e-01;DP=6;ExcessHet=0.0000;FS=4.771;MLEAC=1;MLEAF=0.250;MQ=27.91;MQRankSum=-7.360e-01;QD=12.03;RAW_MQ=2337.00;ReadPosRankSum=0.736;SOR=2.225 GT:AD:DP:GQ:PL 0/0:3,0:3:9:0,9,104 ./. 0/1:1,2:3:26:44,0,26 -chr20 18952365 . G A 119.33 . AC=3;AF=0.750;AN=4;BaseQRankSum=-7.360e-01;ClippingRankSum=0.736;DP=6;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=30.86;MQRankSum=-7.360e-01;QD=19.89;RAW_MQ=5713.00;ReadPosRankSum=0.736;SOR=0.941 GT:AD:DP:GQ:PL 0/1:1,2:3:26:40,0,26 1/1:0,3:3:9:93,9,0 ./. +chr20 18951869 . C T 92.96 . AC=2;AF=0.500;AN=4;DP=8;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=33.61;QD=23.24;RAW_MQ=4518.00;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,4:4:12:107,12,0 ./. 0/0:4,0:4:12:0,12,119 +chr20 18951894 . A T 92.96 . AC=2;AF=0.500;AN=4;DP=8;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=33.61;QD=23.24;RAW_MQ=4518.00;SOR=1.609 GT:AD:DP:GQ:PL 1/1:0,4:4:12:107,12,0 ./. 0/0:4,0:4:12:0,12,119 +chr20 18951906 . A G 36.67 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.736;ClippingRankSum=-7.360e-01;DP=7;ExcessHet=0.0000;FS=4.771;MLEAC=1;MLEAF=0.250;MQ=27.91;MQRankSum=-7.360e-01;QD=12.22;RAW_MQ=2337.00;ReadPosRankSum=0.736;SOR=2.225 GT:AD:DP:GQ:PL 0/0:4,0:4:12:0,12,119 ./. 0/1:1,2:3:26:44,0,26 +chr20 18951975 . G A 36.77 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.736;ClippingRankSum=-7.360e-01;DP=6;ExcessHet=0.0000;FS=4.771;MLEAC=1;MLEAF=0.250;MQ=27.91;MQRankSum=-7.360e-01;QD=12.26;RAW_MQ=2337.00;ReadPosRankSum=0.736;SOR=2.225 GT:AD:DP:GQ:PL 0/0:3,0:3:9:0,9,104 ./. 0/1:1,2:3:26:44,0,26 +chr20 18952365 . G A 121.05 . AC=3;AF=0.750;AN=4;BaseQRankSum=-7.360e-01;ClippingRankSum=0.736;DP=6;ExcessHet=0.0000;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=30.86;MQRankSum=-7.360e-01;QD=20.17;RAW_MQ=5713.00;ReadPosRankSum=0.736;SOR=0.941 GT:AD:DP:GQ:PL 0/1:1,2:3:26:40,0,26 1/1:0,3:3:9:93,9,0 ./. chr20 18952547 . C T 355.97 . AC=6;AF=1.00;AN=6;DP=15;ExcessHet=0.0000;FS=0.000;MLEAC=5;MLEAF=0.833;MQ=35.39;QD=23.73;RAW_MQ=18788.00;SOR=0.818 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 1/1:0,7:7:21:173,21,0 1/1:0,6:6:18:148,18,0 -chr20 18952634 . C T 275.78 . AC=4;AF=1.00;AN=4;DP=11;ExcessHet=0.0000;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=36.23;QD=25.07;RAW_MQ=14436.00;SOR=1.270 GT:AD:DP:GQ:PL ./. 1/1:0,5:5:15:144,15,0 1/1:0,6:6:18:148,18,0 -chr20 18952691 . G C 231.46 . AC=4;AF=1.00;AN=4;DP=8;ExcessHet=0.0000;FS=0.000;MLEAC=3;MLEAF=0.750;MQ=35.94;QD=28.93;RAW_MQ=10336.00;SOR=2.833 GT:AD:DP:GQ:PL ./. 1/1:0,4:4:12:129,12,0 1/1:0,4:4:12:119,12,0 +chr20 18952634 . C T 278.63 . AC=4;AF=1.00;AN=4;DP=11;ExcessHet=0.0000;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=36.23;QD=25.33;RAW_MQ=14436.00;SOR=1.270 GT:AD:DP:GQ:PL ./. 1/1:0,5:5:15:144,15,0 1/1:0,6:6:18:148,18,0 +chr20 18952691 . G C 233.96 . AC=4;AF=1.00;AN=4;DP=8;ExcessHet=0.0000;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=35.94;QD=29.24;RAW_MQ=10336.00;SOR=2.833 GT:AD:DP:GQ:PL ./. 1/1:0,4:4:12:129,12,0 1/1:0,4:4:12:119,12,0 chr20 18953080 . C G 89.10 . AC=2;AF=0.333;AN=6;DP=11;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=40.00;QD=29.70;RAW_MQ=4800.00;SOR=2.833 GT:AD:DP:GQ:PL 0/0:2,0:2:6:0,6,70 0/0:6,0:6:18:0,18,199 1/1:0,3:3:9:104,9,0 chr20 18953220 . A G 1085.71 . AC=6;AF=1.00;AN=6;DP=42;ExcessHet=0.0000;FS=0.000;MLEAC=6;MLEAF=1.00;MQ=34.63;QD=25.85;RAW_MQ=50369.00;SOR=3.716 GT:AD:DP:GQ:PL 1/1:0,11:11:33:284,33,0 1/1:0,22:22:66:582,66,0 1/1:0,9:9:27:233,27,0 chr20 18953616 . G C 144.62 . AC=2;AF=0.333;AN=6;DP=42;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=27.23;QD=29.82;RAW_MQ=2966.00;SOR=3.258 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,4:4:12:1|1:18953616_G_C:161,12,0 0/0:18,0:18:19:.:.:0,19,526 0/0:20,0:20:60:.:.:0,60,585 @@ -3170,7 +3170,7 @@ chr20 18953623 . A T 146.55 . AC=2;AF=0.500;AN=4;DP=44;ExcessHet=0.0000;FS=0.000 chr20 18953626 . C G 121.36 . AC=2;AF=0.500;AN=4;DP=43;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=10.71;QD=28.34;RAW_MQ=2525.00;SOR=2.833 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,3:3:9:1|1:18953616_G_C:135,9,0 ./.:19,0:19:0:.:.:0,0,461 0/0:21,0:21:63:.:.:0,63,589 chr20 18953786 . A AT 73.56 . AC=1;AF=0.167;AN=6;BaseQRankSum=-6.840e-01;ClippingRankSum=0.322;DP=23;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=36.26;MQRankSum=0.684;QD=9.19;RAW_MQ=10520.00;ReadPosRankSum=0.684;SOR=1.270 GT:AD:DP:GQ:PL 0/0:2,0:2:6:0,6,70 0/0:13,0:13:39:0,39,421 0/1:5,3:8:82:82,0,155 chr20 18954100 . T C 1361.89 . AC=5;AF=0.833;AN=6;BaseQRankSum=1.27;ClippingRankSum=-6.350e-01;DP=45;ExcessHet=0.0000;FS=40.599;MLEAC=4;MLEAF=0.667;MQ=38.26;MQRankSum=2.65;QD=30.95;RAW_MQ=65879.00;ReadPosRankSum=-1.694e+00;SOR=7.475 GT:AD:DP:GQ:PL 1/1:0,22:22:66:765,66,0 0/1:3,17:20:23:541,0,23 1/1:0,2:2:6:70,6,0 -chr20 18954158 . G A 183.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.337;ClippingRankSum=-1.107e+00;DP=35;ExcessHet=0.0000;FS=3.274;MLEAC=1;MLEAF=0.250;MQ=37.29;MQRankSum=1.11;QD=10.82;RAW_MQ=25030.00;ReadPosRankSum=-1.107e+00;SOR=2.517 GT:AD:DP:GQ:PL 0/0:17,0:17:48:0,48,720 0/1:9,8:17:99:192,0,249 ./. +chr20 18954158 . G A 184.63 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.337;ClippingRankSum=-1.107e+00;DP=35;ExcessHet=0.0000;FS=3.274;MLEAC=1;MLEAF=0.250;MQ=37.29;MQRankSum=1.11;QD=10.86;RAW_MQ=25030.00;ReadPosRankSum=-1.107e+00;SOR=2.517 GT:AD:DP:GQ:PL 0/0:17,0:17:48:0,48,720 0/1:9,8:17:99:192,0,249 ./. chr20 18954327 . A C 4185.73 . AC=6;AF=1.00;AN=6;DP=96;ExcessHet=0.0000;FS=0.000;MLEAC=6;MLEAF=1.00;MQ=51.92;QD=35.40;RAW_MQ=258832.00;SOR=0.714 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,43:43:99:1|1:18954327_A_C:1903,129,0 1/1:0,34:34:99:1|1:18954327_A_C:1486,102,0 1/1:0,18:18:54:1|1:18954327_A_C:810,54,0 chr20 18954335 . A G 4193.73 . AC=6;AF=1.00;AN=6;DP=96;ExcessHet=0.0000;FS=0.000;MLEAC=6;MLEAF=1.00;MQ=52.51;QD=29.26;RAW_MQ=264741.00;SOR=0.757 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,42:42:99:1|1:18954327_A_C:1878,126,0 1/1:0,34:34:99:1|1:18954327_A_C:1484,102,0 1/1:0,19:19:57:1|1:18954327_A_C:845,57,0 chr20 18954367 . C G 3400.73 . AC=6;AF=1.00;AN=6;DP=106;ExcessHet=0.0000;FS=0.000;MLEAC=6;MLEAF=1.00;MQ=53.12;QD=32.39;RAW_MQ=299077.00;SOR=0.833 GT:AD:DP:GQ:PL 1/1:0,45:45:99:1439,135,0 1/1:0,37:37:99:1236,111,0 1/1:0,23:23:69:739,69,0 @@ -13684,8 +13684,8 @@ chr21 28340356 . A T 528.29 . AC=1;AF=0.167;AN=6;BaseQRankSum=2.48;ClippingRankS chr21 28340557 . T C 596.29 . AC=1;AF=0.167;AN=6;BaseQRankSum=-1.249e+00;ClippingRankSum=0.989;DP=124;ExcessHet=0.0000;FS=2.277;MLEAC=1;MLEAF=0.167;MQ=60.00;MQRankSum=-1.560e-01;QD=11.04;RAW_MQ=194400.00;ReadPosRankSum=0.798;SOR=1.051 GT:AD:DP:GQ:PL 0/1:29,25:54:99:605,0,773 0/0:35,0:35:99:0,99,1245 0/0:35,0:35:99:0,102,1167 chr21 28340638 . G A 2038.95 . AC=3;AF=0.500;AN=6;BaseQRankSum=1.08;ClippingRankSum=0.770;DP=134;ExcessHet=0.0000;FS=4.045;MLEAC=3;MLEAF=0.500;MQ=60.00;MQRankSum=0.538;QD=20.60;RAW_MQ=356400.00;ReadPosRankSum=0.902;SOR=0.438 GT:AD:DP:GQ:PL 0/1:32,24:56:99:586,0,854 0/0:35,0:35:99:0,99,1245 1/1:0,43:43:99:1469,129,0 chr21 28340696 . C CAGAATATATCTTGCAAAACAGAATAACAAATACTATTTTAAATTTGCCATACCCTTAAGCATATATAATCAATAAGTTTCTTTAAATAATTGTTATTTGTA 1639.10 . AC=2;AF=0.333;AN=6;DP=125;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=0.333;MQ=60.00;QD=28.15;RAW_MQ=154800.00;SOR=0.746 GT:AD:DP:GQ:PL 0/0:47,0:47:99:0,120,1800 0/0:35,0:35:99:0,99,1245 1/1:0,37:37:99:1656,107,0 -chr21 28341198 . A T 579.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=-5.560e-01;ClippingRankSum=-6.570e-01;DP=77;ExcessHet=0.0000;FS=8.850;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=1.01;QD=13.81;RAW_MQ=151200.00;ReadPosRankSum=0.758;SOR=0.626 GT:AD:DP:GQ:PL 0/1:19,23:42:99:588,0,515 0/0:35,0:35:99:0,99,1245 ./. -chr21 28341510 . T C 337.91 . AC=1;AF=0.250;AN=4;BaseQRankSum=-1.642e+00;ClippingRankSum=-7.690e-01;DP=65;ExcessHet=0.0000;FS=1.468;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.021;QD=11.26;RAW_MQ=111600.00;ReadPosRankSum=-3.120e-01;SOR=0.340 GT:AD:DP:GQ:PL 0/1:16,14:30:99:346,0,486 0/0:34,0:34:99:0,102,1025 ./. +chr21 28341198 . A T 580.63 . AC=1;AF=0.250;AN=4;BaseQRankSum=-5.560e-01;ClippingRankSum=-6.570e-01;DP=77;ExcessHet=0.0000;FS=8.850;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=1.01;QD=13.82;RAW_MQ=151200.00;ReadPosRankSum=0.758;SOR=0.626 GT:AD:DP:GQ:PL 0/1:19,23:42:99:588,0,515 0/0:35,0:35:99:0,99,1245 ./. +chr21 28341510 . T C 338.63 . AC=1;AF=0.250;AN=4;BaseQRankSum=-1.642e+00;ClippingRankSum=-7.690e-01;DP=65;ExcessHet=0.0000;FS=1.468;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.021;QD=11.29;RAW_MQ=111600.00;ReadPosRankSum=-3.120e-01;SOR=0.340 GT:AD:DP:GQ:PL 0/1:16,14:30:99:346,0,486 0/0:34,0:34:99:0,102,1025 ./. chr21 28342633 . A T 568.29 . AC=1;AF=0.167;AN=6;BaseQRankSum=0.451;ClippingRankSum=0.451;DP=124;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.167;MQ=60.00;MQRankSum=0.055;QD=12.35;RAW_MQ=165600.00;ReadPosRankSum=-6.050e-01;SOR=0.706 GT:AD:DP:GQ:PL 0/1:24,22:46:99:577,0,611 0/0:44,0:44:99:0,105,1317 0/0:34,0:34:99:0,99,1485 chr21 28342723 . T A 1833.95 . AC=3;AF=0.500;AN=6;BaseQRankSum=-5.800e-01;ClippingRankSum=0.603;DP=128;ExcessHet=0.0000;FS=0.945;MLEAC=3;MLEAF=0.500;MQ=60.00;MQRankSum=0.557;QD=22.10;RAW_MQ=302400.00;ReadPosRankSum=1.15;SOR=0.680 GT:AD:DP:GQ:PL 0/1:21,24:45:99:669,0,575 0/0:44,0:44:99:0,105,1317 1/1:0,38:38:99:1181,114,0 chr21 28343113 . T TG 3126.69 . AC=6;AF=1.00;AN=6;DP=101;ExcessHet=0.0000;FS=0.000;MLEAC=6;MLEAF=1.00;MQ=59.92;QD=31.58;RAW_MQ=362601.00;SOR=1.090 GT:AD:DP:GQ:PL 1/1:0,42:42:99:1334,126,0 1/1:0,26:26:78:826,78,0 1/1:0,31:31:93:980,93,0 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksBandedExpected.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksBandedExpected.g.vcf index 957e2433785..4b393adcd24 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksBandedExpected.g.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksBandedExpected.g.vcf @@ -58,28 +58,28 @@ chr20 69772 . AAAGC A, . . BaseQRankSum=0.937;DP=14;MQ=34.15;MQ0=0;MQRa chr20 69773 . A . . END=69774 GT:DP:GQ:MIN_DP:MIN_GQ:PL ./.:7:0:3:0:0,0,0 ./.:7:12:7:15:0,12,180 chr20 69775 . C . . END=69783 GT:DP:GQ:MIN_DP:MIN_GQ:PL ./.:7:0:3:0:0,0,0 ./.:7:15:7:15:0,15,160 chr20 69784 . A . . END=69791 GT:DP:GQ:MIN_DP:MIN_GQ:PL ./. ./.:7:15:7:15:0,15,160 -chr21 1 . G . . END=1999999 GT ./. ./. -chr21 2000000 . N . . END=3999999 GT ./. ./. -chr21 4000000 . N . . END=5999999 GT ./. ./. -chr21 6000000 . C . . END=7999999 GT ./. ./. -chr21 8000000 . G . . END=9999999 GT ./. ./. -chr21 10000000 . C . . END=11999999 GT ./. ./. -chr21 12000000 . N . . END=13999999 GT ./. ./. -chr21 14000000 . T . . END=15999999 GT ./. ./. -chr21 16000000 . A . . END=17999999 GT ./. ./. -chr21 18000000 . G . . END=19999999 GT ./. ./. -chr21 20000000 . A . . END=21999999 GT ./. ./. -chr21 22000000 . T . . END=23999999 GT ./. ./. -chr21 24000000 . G . . END=25999999 GT ./. ./. -chr21 26000000 . G . . END=27999999 GT ./. ./. -chr21 28000000 . C . . END=29999999 GT ./. ./. -chr21 30000000 . G . . END=31999999 GT ./. ./. -chr21 32000000 . A . . END=33999999 GT ./. ./. -chr21 34000000 . T . . END=35999999 GT ./. ./. -chr21 36000000 . G . . END=37999999 GT ./. ./. -chr21 38000000 . A . . END=39999999 GT ./. ./. -chr21 40000000 . T . . END=41999999 GT ./. ./. -chr21 42000000 . G . . END=43999999 GT ./. ./. -chr21 44000000 . G . . END=45999999 GT ./. ./. -chr21 46000000 . G . . END=46709983 GT ./. ./. -chr20_GL383577v2_alt 1 . G . . END=128386 GT ./. ./. +chr21 1 . G . . END=1999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 2000000 . N . . END=3999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 4000000 . N . . END=5999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 6000000 . C . . END=7999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 8000000 . G . . END=9999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 10000000 . C . . END=11999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 12000000 . N . . END=13999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 14000000 . T . . END=15999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 16000000 . A . . END=17999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 18000000 . G . . END=19999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 20000000 . A . . END=21999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 22000000 . T . . END=23999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 24000000 . G . . END=25999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 26000000 . G . . END=27999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 28000000 . C . . END=29999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 30000000 . G . . END=31999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 32000000 . A . . END=33999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 34000000 . T . . END=35999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 36000000 . G . . END=37999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 38000000 . A . . END=39999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 40000000 . T . . END=41999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 42000000 . G . . END=43999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 44000000 . G . . END=45999999 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr21 46000000 . G . . END=46709983 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr20_GL383577v2_alt 1 . G . . END=128386 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksExpected.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksExpected.g.vcf index 3afbbdeba31..380199c9169 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksExpected.g.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/gvcfWithTrailingReferenceBlocksExpected.g.vcf @@ -58,5 +58,5 @@ chr20 69772 . AAAGC A, . . BaseQRankSum=0.937;DP=14;MQ=34.15;MQ0=0;MQRa chr20 69773 . A . . END=69774 GT:DP:GQ:MIN_DP:MIN_GQ:PL ./.:7:0:3:0:0,0,0 ./.:7:12:7:15:0,12,180 chr20 69775 . C . . END=69783 GT:DP:GQ:MIN_DP:MIN_GQ:PL ./.:7:0:3:0:0,0,0 ./.:7:15:7:15:0,15,160 chr20 69784 . A . . END=69791 GT:DP:GQ:MIN_DP:MIN_GQ:PL ./. ./.:7:15:7:15:0,15,160 -chr21 1 . G . . END=46709983 GT ./. ./. -chr20_GL383577v2_alt 1 . G . . END=128386 GT ./. ./. +chr21 1 . G . . END=46709983 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +chr20_GL383577v2_alt 1 . G . . END=128386 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf index 2ba86171701..d41b79cef88 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf @@ -11219,9 +11219,9 @@ 20 10098361 . T . . END=10098380 GT:DP:GQ:MIN_DP:PL ./.:1:0:1:0,0,0 ./.:9:0:2:0,0,0 20 10098381 . T . . END=10098431 GT:DP:GQ:MIN_DP:PL ./.:1:3:1:0,3,37 ./.:9:0:2:0,0,0 20 10098432 . A . . END=10098435 GT:DP:GQ:MIN_DP:PL ./.:1:3:1:0,3,37 ./.:2:3:2:0,3,45 -20 10098436 . A . . END=10098454 GT:DP:GQ:MIN_DP:PL ./.:1:3:1:0,3,37 ./. -20 10098455 . A . . END=10098551 GT ./. ./. -20 10098552 . T . . END=10098572 GT:DP:GQ:MIN_DP:PL ./.:1:3:1:0,3,40 ./. +20 10098436 . A . . END=10098454 GT:DP:GQ:MIN_DP:PL ./.:1:3:1:0,3,37 ./.:0:0:0:0,0,0 +20 10098455 . A . . END=10098551 GT:DP:GQ:MIN_DP:PL ./.:0:0:0:0,0,0 ./.:0:0:0:0,0,0 +20 10098552 . T . . END=10098572 GT:DP:GQ:MIN_DP:PL ./.:1:3:1:0,3,40 ./.:0:0:0:0,0,0 20 10098573 . A . . END=10098574 GT:DP:GQ:MIN_DP:PL ./.:1:3:1:0,3,40 ./.:9:21:9:0,21,315 20 10098575 . A . . END=10098580 GT:DP:GQ:MIN_DP:PL ./.:1:3:1:0,3,40 ./.:10:0:9:0,0,0 20 10098581 . T . . END=10098586 GT:DP:GQ:MIN_DP:PL ./.:1:3:1:0,3,40 ./.:12:27:11:0,27,405 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/tetraploidRun.GATK3.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/tetraploidRun.GATK3.g.vcf index 1b2c26d037a..622f751c8b9 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/tetraploidRun.GATK3.g.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/tetraploidRun.GATK3.g.vcf @@ -8,7 +8,6 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine= ##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=1(exclusive) ##INFO= @@ -19,8 +18,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= -##INFO= ##INFO= ##INFO= ##INFO= @@ -28,97 +25,10 @@ ##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:///humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37_decoy.fasta -##source=CombineGVCFs +##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta ##source=SelectVariants #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00610 HG01187 NA18486 20 4966254 . A . . END=4966255 GT:DP:GQ:MIN_DP:PL ./././.:21:23:20:0,24,57,114,855 ./././.:27:32:26:0,32,78,156,1046 ./././.:44:49:43:0,50,120,241,1800 @@ -297,27 +207,27 @@ 20 4966660 . G . . . GT:DP:GQ:MIN_DP:PL ./././.:2:1:1:0,1,3,6,32 ./././.:11:12:11:0,12,30,60,450 ./././.:6:7:6:0,7,18,36,208 20 4966661 . G . . END=4966662 GT:DP:GQ:MIN_DP:PL ./././.:2:1:1:0,1,3,6,32 ./././.:12:13:11:0,14,33,66,458 ./././.:6:7:6:0,7,18,36,208 20 4966663 . T . . END=4966664 GT:DP:GQ:MIN_DP:PL ./././.:2:1:1:0,1,3,6,32 ./././.:12:13:11:0,14,33,66,458 ./././.:7:8:7:0,9,21,42,236 -20 4966665 . G . . . GT:DP:GQ:MIN_DP:PL ./././. ./././.:12:13:11:0,14,33,66,458 ./././.:7:8:7:0,9,21,42,236 -20 4966666 . G . . END=4966667 GT:DP:GQ:MIN_DP:PL ./././. ./././.:11:12:11:0,12,30,60,450 ./././.:7:8:7:0,9,21,42,236 -20 4966668 . A . . . GT:DP:GQ:MIN_DP:PL ./././. ./././.:11:12:11:0,12,30,60,450 ./././.:7:7:7:0,7,18,36,270 -20 4966669 . A . . END=4966671 GT:DP:GQ:MIN_DP:PL ./././. ./././.:13:14:13:0,15,36,72,540 ./././.:7:7:7:0,7,18,36,270 -20 4966672 . A . . END=4966675 GT:DP:GQ:MIN_DP:PL ./././. ./././.:14:16:13:0,16,39,78,550 ./././.:7:7:7:0,7,18,36,270 -20 4966676 . C . . . GT:DP:GQ:MIN_DP:PL ./././. ./././.:14:16:13:0,16,39,78,550 ./././.:8:8:8:0,9,21,42,315 -20 4966677 . C . . END=4966678 GT:DP:GQ:MIN_DP:PL ./././. ./././.:14:17:14:0,17,42,84,542 ./././.:8:8:8:0,9,21,42,315 -20 4966679 . A . . . GT:DP:GQ:MIN_DP:PL ./././. ./././.:14:17:14:0,17,42,84,542 ./././.:8:9:8:0,10,24,48,283 -20 4966680 . A . . END=4966683 GT:DP:GQ:MIN_DP:PL ./././. ./././.:15:18:15:0,19,45,90,569 ./././.:8:9:8:0,10,24,48,283 -20 4966684 . C . . . GT:DP:GQ:MIN_DP:PL ./././. ./././.:15:17:15:0,17,42,84,630 ./././.:8:9:8:0,10,24,48,283 -20 4966685 . A . . END=4966688 GT:DP:GQ:MIN_DP:PL ./././. ./././.:16:18:16:0,19,45,90,675 ./././.:8:9:8:0,10,24,48,283 -20 4966689 . T . . END=4966690 GT:DP:GQ:MIN_DP:PL ./././. ./././.:16:18:16:0,19,45,90,675 ./././.:10:11:9:0,11,27,54,313 -20 4966691 . C . . . GT:DP:GQ:MIN_DP:PL ./././. ./././.:16:17:16:0,17,42,84,630 ./././.:10:11:9:0,11,27,54,313 -20 4966692 . T . . . GT:DP:GQ:MIN_DP:PL ./././. ./././.:17:18:17:0,19,45,90,675 ./././.:10:11:9:0,11,27,54,313 -20 4966693 . G . . . GT:DP:GQ:MIN_DP:PL ./././. ./././.:17:17:17:0,17,42,84,630 ./././.:10:9:10:0,10,24,48,360 -20 4966694 . G . . . GT:DP:GQ:MIN_DP:PL ./././. ./././.:16:16:16:0,16,39,78,585 ./././.:10:9:10:0,10,24,48,360 -20 4966695 . T . . . GT:DP:GQ:MIN_DP:PL ./././. ./././.:16:16:16:0,16,39,78,585 ./././.:11:11:11:0,11,27,54,405 -20 4966696 . T . . . GT:DP:GQ:MIN_DP:PL ./././. ./././.:16:16:16:0,16,39,78,585 ./././.:13:12:12:0,12,30,60,450 -20 4966697 . T . . END=4966700 GT:DP:GQ:MIN_DP:PL ./././. ./././.:17:17:17:0,17,42,84,630 ./././.:13:12:12:0,12,30,60,450 -20 4966701 . C . . . GT:DP:GQ:MIN_DP:PL ./././. ./././.:19:19:17:0,20,48,96,720 ./././.:13:12:12:0,12,30,60,450 -20 4966702 . A . . END=4966703 GT:DP:GQ:MIN_DP:PL ./././. ./././.:19:19:17:0,20,48,96,720 ./././.:12:13:12:0,14,33,66,495 +20 4966665 . G . . . GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:12:13:11:0,14,33,66,458 ./././.:7:8:7:0,9,21,42,236 +20 4966666 . G . . END=4966667 GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:11:12:11:0,12,30,60,450 ./././.:7:8:7:0,9,21,42,236 +20 4966668 . A . . . GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:11:12:11:0,12,30,60,450 ./././.:7:7:7:0,7,18,36,270 +20 4966669 . A . . END=4966671 GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:13:14:13:0,15,36,72,540 ./././.:7:7:7:0,7,18,36,270 +20 4966672 . A . . END=4966675 GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:14:16:13:0,16,39,78,550 ./././.:7:7:7:0,7,18,36,270 +20 4966676 . C . . . GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:14:16:13:0,16,39,78,550 ./././.:8:8:8:0,9,21,42,315 +20 4966677 . C . . END=4966678 GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:14:17:14:0,17,42,84,542 ./././.:8:8:8:0,9,21,42,315 +20 4966679 . A . . . GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:14:17:14:0,17,42,84,542 ./././.:8:9:8:0,10,24,48,283 +20 4966680 . A . . END=4966683 GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:15:18:15:0,19,45,90,569 ./././.:8:9:8:0,10,24,48,283 +20 4966684 . C . . . GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:15:17:15:0,17,42,84,630 ./././.:8:9:8:0,10,24,48,283 +20 4966685 . A . . END=4966688 GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:16:18:16:0,19,45,90,675 ./././.:8:9:8:0,10,24,48,283 +20 4966689 . T . . END=4966690 GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:16:18:16:0,19,45,90,675 ./././.:10:11:9:0,11,27,54,313 +20 4966691 . C . . . GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:16:17:16:0,17,42,84,630 ./././.:10:11:9:0,11,27,54,313 +20 4966692 . T . . . GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:17:18:17:0,19,45,90,675 ./././.:10:11:9:0,11,27,54,313 +20 4966693 . G . . . GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:17:17:17:0,17,42,84,630 ./././.:10:9:10:0,10,24,48,360 +20 4966694 . G . . . GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:16:16:16:0,16,39,78,585 ./././.:10:9:10:0,10,24,48,360 +20 4966695 . T . . . GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:16:16:16:0,16,39,78,585 ./././.:11:11:11:0,11,27,54,405 +20 4966696 . T . . . GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:16:16:16:0,16,39,78,585 ./././.:13:12:12:0,12,30,60,450 +20 4966697 . T . . END=4966700 GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:17:17:17:0,17,42,84,630 ./././.:13:12:12:0,12,30,60,450 +20 4966701 . C . . . GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:19:19:17:0,20,48,96,720 ./././.:13:12:12:0,12,30,60,450 +20 4966702 . A . . END=4966703 GT:DP:GQ:MIN_DP:PL ./././.:0:0:0:0,0,0,0,0 ./././.:19:19:17:0,20,48,96,720 ./././.:12:13:12:0,14,33,66,495 20 4966704 . G . . END=4966706 GT:DP:GQ:MIN_DP:PL ./././.:1:1:1:0,1,3,6,33 ./././.:19:19:17:0,20,48,96,720 ./././.:12:13:12:0,14,33,66,495 20 4966707 . A . . . GT:DP:GQ:MIN_DP:PL ./././.:1:1:1:0,1,3,6,33 ./././.:19:19:17:0,20,48,96,720 ./././.:12:14:12:0,15,36,72,435 20 4966708 . T . . END=4966709 GT:DP:GQ:MIN_DP:PL ./././.:2:2:2:0,2,6,12,69 ./././.:19:19:17:0,20,48,96,720 ./././.:13:16:13:0,16,39,78,459 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.3.include_nonvariant.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.3.include_nonvariant.vcf index 31d3c0f0e54..b58f48dbcc2 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.3.include_nonvariant.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combine.single.sample.pipeline.3.include_nonvariant.vcf @@ -2263,97 +2263,97 @@ 20 10032140 . G . . . DP=2 GT:DP:RGQ 0/0:2:6 20 10032141 . A . . . DP=2 GT:DP:RGQ 0/0:2:6 20 10032142 . A . . . DP=2 GT:DP:RGQ 0/0:2:6 -20 10032143 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032144 . G . . . . GT:DP:RGQ ./.:0:0 -20 10032145 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032146 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032147 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032148 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032149 . G . . . . GT:DP:RGQ ./.:0:0 -20 10032150 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032151 . C . . . . GT:DP:RGQ ./.:0:0 -20 10032152 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032153 . G . . . . GT:DP:RGQ ./.:0:0 -20 10032154 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032155 . C . . . . GT:DP:RGQ ./.:0:0 -20 10032156 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032157 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032158 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032159 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032160 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032161 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032162 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032163 . G . . . . GT:DP:RGQ ./.:0:0 -20 10032164 . C . . . . GT:DP:RGQ ./.:0:0 -20 10032165 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032166 . G . . . . GT:DP:RGQ ./.:0:0 -20 10032167 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032168 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032169 . C . . . . GT:DP:RGQ ./.:0:0 -20 10032170 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032171 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032172 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032173 . G . . . . GT:DP:RGQ ./.:0:0 -20 10032174 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032175 . G . . . . GT:DP:RGQ ./.:0:0 -20 10032176 . G . . . . GT:DP:RGQ ./.:0:0 -20 10032177 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032178 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032179 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032180 . G . . . . GT:DP:RGQ ./.:0:0 -20 10032181 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032182 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032183 . G . . . . GT:DP:RGQ ./.:0:0 -20 10032184 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032185 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032186 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032187 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032188 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032189 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032190 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032191 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032192 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032193 . G . . . . GT:DP:RGQ ./.:0:0 -20 10032194 . G . . . . GT:DP:RGQ ./.:0:0 -20 10032195 . C . . . . GT:DP:RGQ ./.:0:0 -20 10032196 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032197 . C . . . . GT:DP:RGQ ./.:0:0 -20 10032198 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032199 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032200 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032201 . G . . . . GT:DP:RGQ ./.:0:0 -20 10032202 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032203 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032204 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032205 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032206 . C . . . . GT:DP:RGQ ./.:0:0 -20 10032207 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032208 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032209 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032210 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032211 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032212 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032213 . G . . . . GT:DP:RGQ ./.:0:0 -20 10032214 . C . . . . GT:DP:RGQ ./.:0:0 -20 10032215 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032216 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032217 . C . . . . GT:DP:RGQ ./.:0:0 -20 10032218 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032219 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032220 . G . . . . GT:DP:RGQ ./.:0:0 -20 10032221 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032222 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032223 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032224 . G . . . . GT:DP:RGQ ./.:0:0 -20 10032225 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032226 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032227 . C . . . . GT:DP:RGQ ./.:0:0 -20 10032228 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032229 . C . . . . GT:DP:RGQ ./.:0:0 -20 10032230 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032231 . A . . . . GT:DP:RGQ ./.:0:0 -20 10032232 . T . . . . GT:DP:RGQ ./.:0:0 -20 10032233 . G . . . . GT:DP:RGQ ./.:0:0 +20 10032143 . A . . . . GT ./. +20 10032144 . G . . . . GT ./. +20 10032145 . T . . . . GT ./. +20 10032146 . T . . . . GT ./. +20 10032147 . A . . . . GT ./. +20 10032148 . A . . . . GT ./. +20 10032149 . G . . . . GT ./. +20 10032150 . A . . . . GT ./. +20 10032151 . C . . . . GT ./. +20 10032152 . T . . . . GT ./. +20 10032153 . G . . . . GT ./. +20 10032154 . T . . . . GT ./. +20 10032155 . C . . . . GT ./. +20 10032156 . A . . . . GT ./. +20 10032157 . A . . . . GT ./. +20 10032158 . A . . . . GT ./. +20 10032159 . T . . . . GT ./. +20 10032160 . A . . . . GT ./. +20 10032161 . A . . . . GT ./. +20 10032162 . T . . . . GT ./. +20 10032163 . G . . . . GT ./. +20 10032164 . C . . . . GT ./. +20 10032165 . A . . . . GT ./. +20 10032166 . G . . . . GT ./. +20 10032167 . A . . . . GT ./. +20 10032168 . A . . . . GT ./. +20 10032169 . C . . . . GT ./. +20 10032170 . A . . . . GT ./. +20 10032171 . A . . . . GT ./. +20 10032172 . A . . . . GT ./. +20 10032173 . G . . . . GT ./. +20 10032174 . A . . . . GT ./. +20 10032175 . G . . . . GT ./. +20 10032176 . G . . . . GT ./. +20 10032177 . T . . . . GT ./. +20 10032178 . T . . . . GT ./. +20 10032179 . T . . . . GT ./. +20 10032180 . G . . . . GT ./. +20 10032181 . A . . . . GT ./. +20 10032182 . A . . . . GT ./. +20 10032183 . G . . . . GT ./. +20 10032184 . A . . . . GT ./. +20 10032185 . A . . . . GT ./. +20 10032186 . A . . . . GT ./. +20 10032187 . A . . . . GT ./. +20 10032188 . A . . . . GT ./. +20 10032189 . T . . . . GT ./. +20 10032190 . T . . . . GT ./. +20 10032191 . A . . . . GT ./. +20 10032192 . T . . . . GT ./. +20 10032193 . G . . . . GT ./. +20 10032194 . G . . . . GT ./. +20 10032195 . C . . . . GT ./. +20 10032196 . A . . . . GT ./. +20 10032197 . C . . . . GT ./. +20 10032198 . A . . . . GT ./. +20 10032199 . A . . . . GT ./. +20 10032200 . A . . . . GT ./. +20 10032201 . G . . . . GT ./. +20 10032202 . T . . . . GT ./. +20 10032203 . T . . . . GT ./. +20 10032204 . T . . . . GT ./. +20 10032205 . A . . . . GT ./. +20 10032206 . C . . . . GT ./. +20 10032207 . A . . . . GT ./. +20 10032208 . A . . . . GT ./. +20 10032209 . T . . . . GT ./. +20 10032210 . T . . . . GT ./. +20 10032211 . T . . . . GT ./. +20 10032212 . A . . . . GT ./. +20 10032213 . G . . . . GT ./. +20 10032214 . C . . . . GT ./. +20 10032215 . A . . . . GT ./. +20 10032216 . A . . . . GT ./. +20 10032217 . C . . . . GT ./. +20 10032218 . T . . . . GT ./. +20 10032219 . T . . . . GT ./. +20 10032220 . G . . . . GT ./. +20 10032221 . A . . . . GT ./. +20 10032222 . T . . . . GT ./. +20 10032223 . A . . . . GT ./. +20 10032224 . G . . . . GT ./. +20 10032225 . A . . . . GT ./. +20 10032226 . A . . . . GT ./. +20 10032227 . C . . . . GT ./. +20 10032228 . T . . . . GT ./. +20 10032229 . C . . . . GT ./. +20 10032230 . T . . . . GT ./. +20 10032231 . A . . . . GT ./. +20 10032232 . T . . . . GT ./. +20 10032233 . G . . . . GT ./. 20 10032234 . A . . . DP=2 GT:DP:RGQ 0/0:2:6 20 10032235 . A . . . DP=2 GT:DP:RGQ 0/0:2:6 20 10032236 . A . . . DP=2 GT:DP:RGQ 0/0:2:6 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combined.single.sample.pipeline.include_nonvariant.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combined.single.sample.pipeline.include_nonvariant.vcf index 01b40dac27c..bb8487740a7 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combined.single.sample.pipeline.include_nonvariant.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/combined.single.sample.pipeline.include_nonvariant.vcf @@ -967,7 +967,7 @@ 20 10030928 . G . . . DP=2 GT:DP:RGQ ./. ./. 0/0:2:6 20 10030929 . A . . . DP=2 GT:DP:RGQ ./. ./. 0/0:2:6 20 10030930 . C . . . DP=2 GT:DP:RGQ ./. ./. 0/0:2:6 -20 10030931 . C A 67.32 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=33.66;RAW_MQ=7200.00;SOR=2.303 GT:AD:DP:GQ:PL ./. ./. 1/1:0,2:2:6:79,6,0 +20 10030931 . C A 69.24 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.62;RAW_MQ=7200.00;SOR=2.303 GT:AD:DP:GQ:PL ./. ./. 1/1:0,2:2:6:79,6,0 20 10030932 . G . . . DP=2 GT:DP:RGQ ./. ./. 0/0:2:6 20 10030933 . A . . . DP=2 GT:DP:RGQ ./. ./. 0/0:2:6 20 10030934 . A . . . DP=2 GT:DP:RGQ ./. ./. 0/0:2:6 @@ -1834,7 +1834,7 @@ 20 10031795 . G . . . DP=2 GT:DP:RGQ ./.:2:0 ./. ./. 20 10031796 . T . . . DP=2 GT:DP:RGQ ./.:2:0 ./. ./. 20 10031797 . A . . . DP=2 GT:DP:RGQ ./.:2:0 ./. ./. -20 10031798 . G A 37.32 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.00;QD=18.66;RAW_MQ=2738.00;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 ./. ./. +20 10031798 . G A 39.24 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=37.00;QD=19.62;RAW_MQ=2738.00;SOR=0.693 GT:AD:DP:GQ:PL 1/1:0,2:2:6:49,6,0 ./. ./. 20 10031799 . T . . . . GT ./. ./. ./. 20 10031800 . T . . . . GT ./. ./. ./. 20 10031801 . A . . . . GT ./. ./. ./. @@ -2179,97 +2179,97 @@ 20 10032140 . G . . . DP=2 GT:DP:RGQ 0/0:2:6 ./. ./. 20 10032141 . A . . . DP=2 GT:DP:RGQ 0/0:2:6 ./. ./. 20 10032142 . A . . . DP=2 GT:DP:RGQ 0/0:2:6 ./. ./. -20 10032143 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032144 . G . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032145 . T . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032146 . T . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032147 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032148 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032149 . G . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032150 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032151 . C . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032152 . T . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032153 . G . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032154 . T . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032155 . C . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032156 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032157 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032158 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032159 . T . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032160 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032161 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032162 . T . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032163 . G . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032164 . C . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032165 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032166 . G . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032167 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032168 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032169 . C . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032170 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032171 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032172 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032173 . G . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032174 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032175 . G . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032176 . G . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032177 . T . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032178 . T . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032179 . T . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032180 . G . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032181 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032182 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032183 . G . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032184 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032185 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032186 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032187 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032188 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032189 . T . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032190 . T . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032191 . A . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032192 . T . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032193 . G . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032194 . G . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032195 . C . . . . GT:DP:RGQ ./.:0:0 ./. ./. -20 10032196 . A . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032197 . C . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032198 . A . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032199 . A . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032200 . A . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032201 . G . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032202 . T . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032203 . T . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032204 . T . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032205 . A . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032206 . C . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032207 . A . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032208 . A . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032209 . T . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032210 . T . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032211 . T . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032212 . A . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032213 . G . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032214 . C . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032215 . A . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032216 . A . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032217 . C . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032218 . T . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032219 . T . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032220 . G . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032221 . A . . . DP=2 GT:DP:RGQ ./.:0:0 0/0:2:6 ./. -20 10032222 . T . . . DP=4 GT:DP:RGQ ./.:0:0 0/0:2:6 0/0:2:6 -20 10032223 . A . . . DP=4 GT:DP:RGQ ./.:0:0 0/0:2:6 0/0:2:6 -20 10032224 . G . . . DP=4 GT:DP:RGQ ./.:0:0 0/0:2:6 0/0:2:6 -20 10032225 . A . . . DP=4 GT:DP:RGQ ./.:0:0 0/0:2:6 0/0:2:6 -20 10032226 . A . . . DP=4 GT:DP:RGQ ./.:0:0 0/0:2:6 0/0:2:6 -20 10032227 . C . . . DP=4 GT:DP:RGQ ./.:0:0 0/0:2:6 0/0:2:6 -20 10032228 . T . . . DP=4 GT:DP:RGQ ./.:0:0 0/0:2:6 0/0:2:6 -20 10032229 . C . . . DP=4 GT:DP:RGQ ./.:0:0 0/0:2:6 0/0:2:6 -20 10032230 . T . . . DP=4 GT:DP:RGQ ./.:0:0 0/0:2:6 0/0:2:6 -20 10032231 . A . . . DP=4 GT:DP:RGQ ./.:0:0 0/0:2:6 0/0:2:6 -20 10032232 . T . . . DP=4 GT:DP:RGQ ./.:0:0 0/0:2:6 0/0:2:6 -20 10032233 . G . . . DP=4 GT:DP:RGQ ./.:0:0 0/0:2:6 0/0:2:6 +20 10032143 . A . . . . GT ./. ./. ./. +20 10032144 . G . . . . GT ./. ./. ./. +20 10032145 . T . . . . GT ./. ./. ./. +20 10032146 . T . . . . GT ./. ./. ./. +20 10032147 . A . . . . GT ./. ./. ./. +20 10032148 . A . . . . GT ./. ./. ./. +20 10032149 . G . . . . GT ./. ./. ./. +20 10032150 . A . . . . GT ./. ./. ./. +20 10032151 . C . . . . GT ./. ./. ./. +20 10032152 . T . . . . GT ./. ./. ./. +20 10032153 . G . . . . GT ./. ./. ./. +20 10032154 . T . . . . GT ./. ./. ./. +20 10032155 . C . . . . GT ./. ./. ./. +20 10032156 . A . . . . GT ./. ./. ./. +20 10032157 . A . . . . GT ./. ./. ./. +20 10032158 . A . . . . GT ./. ./. ./. +20 10032159 . T . . . . GT ./. ./. ./. +20 10032160 . A . . . . GT ./. ./. ./. +20 10032161 . A . . . . GT ./. ./. ./. +20 10032162 . T . . . . GT ./. ./. ./. +20 10032163 . G . . . . GT ./. ./. ./. +20 10032164 . C . . . . GT ./. ./. ./. +20 10032165 . A . . . . GT ./. ./. ./. +20 10032166 . G . . . . GT ./. ./. ./. +20 10032167 . A . . . . GT ./. ./. ./. +20 10032168 . A . . . . GT ./. ./. ./. +20 10032169 . C . . . . GT ./. ./. ./. +20 10032170 . A . . . . GT ./. ./. ./. +20 10032171 . A . . . . GT ./. ./. ./. +20 10032172 . A . . . . GT ./. ./. ./. +20 10032173 . G . . . . GT ./. ./. ./. +20 10032174 . A . . . . GT ./. ./. ./. +20 10032175 . G . . . . GT ./. ./. ./. +20 10032176 . G . . . . GT ./. ./. ./. +20 10032177 . T . . . . GT ./. ./. ./. +20 10032178 . T . . . . GT ./. ./. ./. +20 10032179 . T . . . . GT ./. ./. ./. +20 10032180 . G . . . . GT ./. ./. ./. +20 10032181 . A . . . . GT ./. ./. ./. +20 10032182 . A . . . . GT ./. ./. ./. +20 10032183 . G . . . . GT ./. ./. ./. +20 10032184 . A . . . . GT ./. ./. ./. +20 10032185 . A . . . . GT ./. ./. ./. +20 10032186 . A . . . . GT ./. ./. ./. +20 10032187 . A . . . . GT ./. ./. ./. +20 10032188 . A . . . . GT ./. ./. ./. +20 10032189 . T . . . . GT ./. ./. ./. +20 10032190 . T . . . . GT ./. ./. ./. +20 10032191 . A . . . . GT ./. ./. ./. +20 10032192 . T . . . . GT ./. ./. ./. +20 10032193 . G . . . . GT ./. ./. ./. +20 10032194 . G . . . . GT ./. ./. ./. +20 10032195 . C . . . . GT ./. ./. ./. +20 10032196 . A . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032197 . C . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032198 . A . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032199 . A . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032200 . A . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032201 . G . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032202 . T . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032203 . T . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032204 . T . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032205 . A . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032206 . C . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032207 . A . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032208 . A . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032209 . T . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032210 . T . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032211 . T . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032212 . A . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032213 . G . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032214 . C . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032215 . A . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032216 . A . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032217 . C . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032218 . T . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032219 . T . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032220 . G . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032221 . A . . . DP=2 GT:DP:RGQ ./. 0/0:2:6 ./. +20 10032222 . T . . . DP=4 GT:DP:RGQ ./. 0/0:2:6 0/0:2:6 +20 10032223 . A . . . DP=4 GT:DP:RGQ ./. 0/0:2:6 0/0:2:6 +20 10032224 . G . . . DP=4 GT:DP:RGQ ./. 0/0:2:6 0/0:2:6 +20 10032225 . A . . . DP=4 GT:DP:RGQ ./. 0/0:2:6 0/0:2:6 +20 10032226 . A . . . DP=4 GT:DP:RGQ ./. 0/0:2:6 0/0:2:6 +20 10032227 . C . . . DP=4 GT:DP:RGQ ./. 0/0:2:6 0/0:2:6 +20 10032228 . T . . . DP=4 GT:DP:RGQ ./. 0/0:2:6 0/0:2:6 +20 10032229 . C . . . DP=4 GT:DP:RGQ ./. 0/0:2:6 0/0:2:6 +20 10032230 . T . . . DP=4 GT:DP:RGQ ./. 0/0:2:6 0/0:2:6 +20 10032231 . A . . . DP=4 GT:DP:RGQ ./. 0/0:2:6 0/0:2:6 +20 10032232 . T . . . DP=4 GT:DP:RGQ ./. 0/0:2:6 0/0:2:6 +20 10032233 . G . . . DP=4 GT:DP:RGQ ./. 0/0:2:6 0/0:2:6 20 10032234 . A . . . DP=6 GT:DP:RGQ 0/0:2:6 0/0:2:6 0/0:2:6 20 10032235 . A . . . DP=6 GT:DP:RGQ 0/0:2:6 0/0:2:6 0/0:2:6 20 10032236 . A . . . DP=6 GT:DP:RGQ 0/0:2:6 0/0:2:6 0/0:2:6 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/includeLowQualSites.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/includeLowQualSites.vcf index b4c85a7264e..9367e5e9874 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/includeLowQualSites.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/includeLowQualSites.vcf @@ -40,7 +40,7 @@ 20 10012731 . C . . . DP=4 GT:DP:RGQ 0/0:2:6 ./. 0/0:2:6 20 10012732 . A . . . DP=4 GT:DP:RGQ 0/0:2:6 ./. 0/0:2:6 20 10012733 . G . . . DP=4 GT:DP:RGQ 0/0:2:6 ./. 0/0:2:6 -20 10012734 . G . 0.03 LowQual DP=4;ExcessHet=3.01;MLEAC=.;MLEAF=.;MQ=NaN;RAW_MQ=7200.00 GT:DP:RGQ 0/0:2:6 0/0 0/0:2:6 +20 10012734 . G . 0.02 LowQual DP=4;ExcessHet=3.01;MLEAC=.;MLEAF=.;MQ=NaN;RAW_MQ=7200.00 GT:DP:RGQ 0/0:2:6 ./. 0/0:2:6 20 10012735 . C . . . DP=4 GT:DP:RGQ 0/0:2:6 ./. 0/0:2:6 20 10012736 . A . . . DP=4 GT:DP:RGQ 0/0:2:6 ./. 0/0:2:6 20 10012737 . G . . . DP=4 GT:DP:RGQ 0/0:2:6 ./. 0/0:2:6 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/testSpanningDeletion.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/testSpanningDeletion.vcf index 91e69061e20..378e733b96b 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/testSpanningDeletion.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/expected/testSpanningDeletion.vcf @@ -36,8 +36,8 @@ ##contig= ##reference=file:///Users/cnorman/projects/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT GTEX-OXRP-0003 GTEX-QXCU-0004 GTEX-RVPV-0003 -20 10096905 . TA T 78.28 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=25.36;RAW_MQ=7200.00;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:6:1|1:10096899_G_T:90,6,0 ./. ./. -20 10096906 . A * 0 LowQual AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;QD=-0.00;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:6:1|1:10096899_G_T:90,6,0 ./. ./. +20 10096905 . TA T 80.18 . AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=25.36;RAW_MQ=7200.00;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:6:1|1:10096899_G_T:90,6,0 ./. ./. +20 10096906 . A * 0 LowQual AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;QD=-0.00;SOR=0.693 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,2:2:6:1|1:10096899_G_T:90,6,0 ./. ./. 20 10096907 . A . . . DP=2 GT:DP:RGQ ./.:2:0 ./. ./. 20 10624924 . TCA T 169.53 . AC=2;AF=0.500;AN=4;BaseQRankSum=0.103;ClippingRankSum=0.00;DP=56;ExcessHet=0.9691;FS=1.657;MLEAC=2;MLEAF=0.500;MQ=50.41;MQRankSum=0.754;QD=5.30;RAW_MQ=142331.00;ReadPosRankSum=120.50;SOR=0.287 GT:AD:DP:GQ:PGT:PID:PL 0/1:11,4:15:71:.:.:71,0,257 ./.:9,0:9:0:.:.:0,0,231 0/1:11,6:17:99:0|1:10624924_TCA_T:107,0,318 20 10624925 . C * 0 LowQual AC=2;AF=0.333;AN=6;DP=64;ExcessHet=0.9691;FS=1.657;MLEAC=2;MLEAF=0.333;QD=0.00;SOR=0.287 GT:AD:DP:GQ:PGT:PID:PL 0/1:11,4:15:71:.:.:71,0,257 0/0:17,0:17:13:.:.:0,13,557 0/1:11,6:17:99:0|1:10624924_TCA_T:107,0,318 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiSamples.GATK3expected.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiSamples.GATK3expected.g.vcf index 1fc9f097bbf..d94e6bcc6fa 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiSamples.GATK3expected.g.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/multiSamples.GATK3expected.g.vcf @@ -137,8 +137,8 @@ ##contig= ##reference=file:///humgen/1kg/reference/human_g1k_v37.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA12891 NA12892 Sample1 Sample10 Sample11 Sample12 Sample13 Sample14 Sample15 Sample16 Sample17 Sample18 Sample19 Sample2 Sample20 Sample21 Sample3 Sample4 Sample5 Sample6 Sample7 Sample8 Sample9 -20 899928 . G C 4944.58 . AC=21;AF=0.808;AN=26;AS_BaseQRankSum=-1.400;AS_FS=0.000;AS_InbreedingCoeff=0.5339;AS_MQ=43.54;AS_MQRankSum=-0.700;AS_QD=25.36;AS_ReadPosRankSum=0.000;AS_SOR=1.863;BaseQRankSum=-1.383e+00;ClippingRankSum=0.00;DP=133;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.5089;MLEAC=25;MLEAF=0.962;MQ=42.34;MQRankSum=-6.740e-01;QD=28.73;RAW_MQ=222270.00;ReadPosRankSum=0.00;SOR=1.781 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,3:3:9:1|1:899928_G_C:135,9,0 1/1:0,18:18:54:1|1:899928_G_C:767,54,0 1/1:0,15:15:45:1|1:899928_G_C:640,45,0 ./. ./. ./. ./. 1/1:0,9:9:27:1|1:899928_G_C:370,27,0 1/1:0,1:1:3:1|1:899928_G_C:45,3,0 ./.:1,0:1:0:.:.:0,0,0 ./.:2,0:2:0:.:.:0,0,0 ./.:3,0:3:0:.:.:0,0,0 1/1:0,5:5:15:1|1:899928_G_C:225,15,0 ./. 0/1:2,2:4:78:0|1:899928_G_C:78,0,282 ./. 1/1:0,51:51:99:1|1:899928_G_C:2229,153,0 1/1:0,3:3:9:1|1:899928_G_C:135,9,0 ./.:2,0:2:0:.:.:0,0,0 0/0:7,0:7:21:.:.:0,21,236 1/1:0,4:4:12:1|1:899928_G_C:168,12,0 1/1:0,2:2:6:1|1:899928_G_C:90,6,0 ./. 0/0:2,0:2:6:.:.:0,6,65 -20 899933 . 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AC=19,2;AF=0.731,0.077;AN=26;AS_BaseQRankSum=-1.000,.;AS_FS=0.000,0.000;AS_InbreedingCoeff=0.5390,0.3914;AS_MQ=40.57,0.00;AS_MQRankSum=-0.700,.;AS_QD=27.24,16.00;AS_ReadPosRankSum=0.000,.;AS_SOR=1.775,0.105;BaseQRankSum=-9.670e-01;ClippingRankSum=0.00;DP=126;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.5566;MLEAC=25,1;MLEAF=0.962,0.038;MQ=39.50;MQRankSum=-6.740e-01;QD=28.20;RAW_MQ=184116.00;ReadPosRankSum=0.00;SOR=1.697 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,3,0:3:9:1|1:899928_G_C:135,9,0,135,9,135 1/1:0,15,0:15:45:1|1:899928_G_C:675,45,0,675,45,675 1/1:0,15,0:15:43:1|1:899928_G_C:633,43,0,633,43,633 ./. ./. ./. ./.:1,0,0:1:0:.:.:0,0,0,0,0,0 1/1:0,8,0:8:24:1|1:899928_G_C:360,24,0,360,24,360 2/2:0,0,1:1:3:1|1:899928_G_C:45,45,45,3,3,0 ./.:1,0,0:1:0:.:.:0,0,0,0,0,0 ./.:2,0,0:2:0:.:.:0,0,0,0,0,0 ./.:1,0,0:1:0:.:.:0,0,0,0,0,0 1/1:0,6,0:6:18:1|1:899928_G_C:270,18,0,270,18,270 ./. 0/1:2,2,0:4:78:0|1:899928_G_C:78,0,282,84,288,372 ./. 1/1:0,48,0:48:99:1|1:899928_G_C:2194,147,0,2194,147,2194 1/1:0,4,0:4:12:1|1:899928_G_C:180,12,0,180,12,180 ./.:2,0,0:2:0:.:.:0,0,0,0,0,0 0/0:7,0,0:7:9:.:.:0,9,182,9,182,182 1/1:0,4,0:4:12:1|1:899928_G_C:180,12,0,180,12,180 1/1:0,2,0:2:6:1|1:899928_G_C:90,6,0,90,6,90 ./. 0/0:1,0,0:1:3:.:.:0,3,36,3,36,36 -20 899938 . G C,* 4855.49 . AC=19,2;AF=0.731,0.077;AN=26;AS_BaseQRankSum=-1.400,.;AS_FS=0.000,0.000;AS_InbreedingCoeff=0.5553,0.4090;AS_MQ=40.66,0.00;AS_MQRankSum=-0.700,.;AS_QD=25.00,16.00;AS_ReadPosRankSum=0.000,.;AS_SOR=1.900,0.105;BaseQRankSum=-1.383e+00;ClippingRankSum=0.00;DP=124;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.5704;MLEAC=25,1;MLEAF=0.962,0.038;MQ=39.58;MQRankSum=-6.740e-01;QD=29.56;RAW_MQ=183275.00;ReadPosRankSum=0.00;SOR=1.811 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,3,0:3:9:1|1:899928_G_C:135,9,0,135,9,135 1/1:0,14,0:14:45:1|1:899928_G_C:675,45,0,675,45,675 1/1:0,15,0:15:43:1|1:899928_G_C:633,43,0,633,43,633 ./. ./. ./. ./.:1,0,0:1:0:.:.:0,0,0,0,0,0 1/1:0,8,0:8:24:1|1:899928_G_C:360,24,0,360,24,360 2/2:0,0,1:1:3:1|1:899928_G_C:45,45,45,3,3,0 ./.:1,0,0:1:0:.:.:0,0,0,0,0,0 ./.:2,0,0:2:0:.:.:0,0,0,0,0,0 ./.:1,0,0:1:0:.:.:0,0,0,0,0,0 1/1:0,6,0:6:18:1|1:899928_G_C:270,18,0,270,18,270 ./. 0/1:2,2,0:4:78:0|1:899928_G_C:78,0,282,84,288,372 ./. 1/1:0,48,0:48:99:1|1:899928_G_C:2194,147,0,2194,147,2194 1/1:0,4,0:4:12:1|1:899928_G_C:180,12,0,180,12,180 ./.:2,0,0:2:0:.:.:0,0,0,0,0,0 0/0:6,0,0:6:15:.:.:0,15,225,15,225,225 1/1:0,4,0:4:12:1|1:899928_G_C:180,12,0,180,12,180 1/1:0,2,0:2:6:1|1:899928_G_C:90,6,0,90,6,90 ./. 0/0:1,0,0:1:3:.:.:0,3,36,3,36,36 -20 899942 . G A 4885.37 . AC=19;AF=0.792;AN=24;AS_BaseQRankSum=0.400;AS_FS=0.000;AS_InbreedingCoeff=0.5567;AS_MQ=44.39;AS_MQRankSum=-0.300;AS_QD=30.62;AS_ReadPosRankSum=-1.500;AS_SOR=1.893;BaseQRankSum=0.493;ClippingRankSum=0.00;DP=148;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.5082;MLEAC=26;MLEAF=1.00;MQ=43.13;MQRankSum=-2.530e-01;QD=28.17;RAW_MQ=264157.00;ReadPosRankSum=-1.501e+00;SOR=1.923 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,3:3:9:1|1:899928_G_C:135,9,0 1/1:0,15:15:45:1|1:899928_G_C:636,45,0 1/1:0,16:16:45:1|1:899928_G_C:636,45,0 ./. ./. ./. ./.:1,0:1:0:.:.:0,0,0 1/1:0,9:9:27:1|1:899928_G_C:366,27,0 ./.:3,0:3:0:.:.:0,0,0 ./.:.:0:0:.:.:0,0,0 ./.:2,0:2:0:.:.:0,0,0 ./.:1,0:1:0:.:.:0,0,0 1/1:0,7:7:19:1|1:899928_G_C:273,19,0 ./. 0/1:2,8:10:88:0|1:899928_G_C:88,0,274 ./. 1/1:0,58:58:99:1|1:899928_G_C:2217,159,0 1/1:0,5:5:13:1|1:899928_G_C:183,13,0 ./.:2,0:2:0:.:.:0,0,0 0/0:5,0:5:15:.:.:0,15,178 1/1:0,7:7:16:1|1:899928_G_C:189,16,0 1/1:0,2:2:6:1|1:899928_G_C:90,6,0 ./. 0/0:1,0:1:3:.:.:0,3,36 +20 899928 . G C 4973.12 . AC=21;AF=0.808;AN=26;AS_BaseQRankSum=-1.400;AS_FS=0.000;AS_InbreedingCoeff=0.5339;AS_MQ=43.54;AS_MQRankSum=-0.700;AS_QD=25.36;AS_ReadPosRankSum=0.000;AS_SOR=1.863;BaseQRankSum=-1.383e+00;ClippingRankSum=0.00;DP=133;ExcessHet=0.0000;FS=0.000;InbreedingCoeff=0.5089;MLEAC=29;MLEAF=1.00;MQ=42.34;MQRankSum=-6.740e-01;QD=28.73;RAW_MQ=222270.00;ReadPosRankSum=0.00;SOR=1.781 GT:AD:DP:GQ:PGT:PID:PL 1/1:0,3:3:9:1|1:899928_G_C:135,9,0 1/1:0,18:18:54:1|1:899928_G_C:767,54,0 1/1:0,15:15:45:1|1:899928_G_C:640,45,0 ./. ./. ./. ./. 1/1:0,9:9:27:1|1:899928_G_C:370,27,0 1/1:0,1:1:3:1|1:899928_G_C:45,3,0 ./.:1,0:1:0:.:.:0,0,0 ./.:2,0:2:0:.:.:0,0,0 ./.:3,0:3:0:.:.:0,0,0 1/1:0,5:5:15:1|1:899928_G_C:225,15,0 ./. 0/1:2,2:4:78:0|1:899928_G_C:78,0,282 ./. 1/1:0,51:51:99:1|1:899928_G_C:2229,153,0 1/1:0,3:3:9:1|1:899928_G_C:135,9,0 ./.:2,0:2:0:.:.:0,0,0 0/0:7,0:7:21:.:.:0,21,236 1/1:0,4:4:12:1|1:899928_G_C:168,12,0 1/1:0,2:2:6:1|1:899928_G_C:90,6,0 ./. 0/0:2,0:2:6:.:.:0,6,65 +20 899933 . 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G C,* 4882.54 . 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