Fix ALL tests???

broadinstitute · Apr 5, 2024 · 6d060ce · 6d060ce
1 parent 0fd8ac2
commit 6d060ce
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Showing 14 changed files with 279 additions and 409 deletions.
diff --git 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<Genotype> 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<Allele> 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<Allele> 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/...va/org/broadinstitute/hellbender/tools/walkers/gnarlyGenotyper/GnarlyGenotyperEngine.java b/...va/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<Allele> 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
@@ -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/...ute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriorsIntegrationTest.java b/...ute/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<VariantContext> expectedVC = VariantContextTestUtils.getVariantContexts(expected);
-        final List<VariantContext> 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<VariantContext> expectedVC = VariantContextTestUtils.getVariantContexts(expected);
-        final List<VariantContext> 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
@@ -3155,22 +3155,22 @@ 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
 chr20	18953623	.	A	T	146.55	.	AC=2;AF=0.500;AN=4;DP=44;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=10.48;QD=29.80;RAW_MQ=2525.00;SOR=2.833	GT:AD:DP:GQ:PGT:PID:PL	1/1:0,3:3:12:1|1:18953616_G_C:161,12,0	./.:20,0:20:0:.:.:0,0,437	0/0:21,0:21:38:.:.:0,38,530
 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