diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerUtils.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerUtils.java index ca2db3eb5ba..90929b70e52 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerUtils.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/AssemblyBasedCallerUtils.java @@ -206,7 +206,8 @@ public static CachingIndexedFastaSequenceFile createReferenceReader(final String * @return never {@code null}. */ public static ReadLikelihoodCalculationEngine createLikelihoodCalculationEngine(final LikelihoodEngineArgumentCollection likelihoodArgs) { - final double log10GlobalReadMismappingRate = likelihoodArgs.phredScaledGlobalReadMismappingRate < 0 ? - Double.MAX_VALUE + //AlleleLikelihoods::normalizeLikelihoods uses Double.NEGATIVE_INFINITY as a flag to disable capping + final double log10GlobalReadMismappingRate = likelihoodArgs.phredScaledGlobalReadMismappingRate < 0 ? Double.NEGATIVE_INFINITY : QualityUtils.qualToErrorProbLog10(likelihoodArgs.phredScaledGlobalReadMismappingRate); switch ( likelihoodArgs.likelihoodEngineImplementation) { diff --git a/src/main/java/org/broadinstitute/hellbender/utils/genotyper/AlleleLikelihoods.java b/src/main/java/org/broadinstitute/hellbender/utils/genotyper/AlleleLikelihoods.java index 9e25781a972..54dc82c796b 100644 --- a/src/main/java/org/broadinstitute/hellbender/utils/genotyper/AlleleLikelihoods.java +++ b/src/main/java/org/broadinstitute/hellbender/utils/genotyper/AlleleLikelihoods.java @@ -352,9 +352,10 @@ public void normalizeLikelihoods(final double maximumLikelihoodDifferenceCap) { private void normalizeLikelihoodsPerEvidence(final double maximumBestAltLikelihoodDifference, final double[][] sampleValues, final int sampleIndex, final int evidenceIndex) { - final BestAllele bestAlternativeAllele = searchBestAllele(sampleIndex,evidenceIndex,false); + //allow the best allele to be the reference because asymmetry leads to strange artifacts like het calls with >90% alt reads + final BestAllele bestAllele = searchBestAllele(sampleIndex,evidenceIndex,true); - final double worstLikelihoodCap = bestAlternativeAllele.likelihood + maximumBestAltLikelihoodDifference; + final double worstLikelihoodCap = bestAllele.likelihood + maximumBestAltLikelihoodDifference; final int alleleCount = alleles.numberOfAlleles(); diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFsIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFsIntegrationTest.java index c6e8d70a122..3af8a246d5a 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFsIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFsIntegrationTest.java @@ -33,6 +33,12 @@ import java.util.stream.Collectors; public class CombineGVCFsIntegrationTest extends CommandLineProgramTest { + // If true, update the expected outputs in tests that assert an exact match vs. prior output, + // instead of actually running the tests. Can be used with "./gradlew test -Dtest.single=HaplotypeCallerIntegrationTest" + // to update all of the exact-match tests at once. After you do this, you should look at the + // diffs in the new expected outputs in git to confirm that they are consistent with expectations. + public static final boolean UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS = false; + private static final List NO_EXTRA_ARGS = Collections.emptyList(); private static final List ATTRIBUTES_TO_IGNORE = Arrays.asList( "RAW_MQ", //MQ data format and key have changed since GATK3 @@ -49,6 +55,14 @@ private static void assertForEachElementInLists(final List actual, final } } + /* + * Make sure that someone didn't leave the UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS toggle turned on + */ + @Test + public void assertThatExpectedOutputUpdateToggleIsDisabled() { + Assert.assertFalse(UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS, "The toggle to update expected outputs should not be left enabled"); + } + @DataProvider public Object[][] gvcfsToCombine() { return new Object[][]{ @@ -134,8 +148,8 @@ public void compareToGATK3(File[] inputs, File outputFile, List extraArg } @Test(dataProvider = "gvcfsToCombine") - public void compareToGATK3ExpectedResults(File[] inputs, File outputFile, List extraArgs, String reference) throws IOException, NoSuchAlgorithmException { - assertVariantContextsMatch(Arrays.asList(inputs), outputFile, extraArgs, reference, ATTRIBUTES_TO_IGNORE); + public void compareToExpectedResults(File[] inputs, File expected, List extraArgs, String reference) throws IOException, NoSuchAlgorithmException { + assertVariantContextsMatch(Arrays.asList(inputs), expected, extraArgs, reference, ATTRIBUTES_TO_IGNORE); } public static void runProcess(ProcessController processController, String[] command) { @@ -161,7 +175,7 @@ public void runCombineGVCFSandAssertSomething(List inputs, File expected, final ArgumentsBuilder args = new ArgumentsBuilder(); args.addReference(new File(reference)) - .addOutput(output); + .addOutput(UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS ? expected : output); for (File input: inputs) { args.addArgument("V", input.getAbsolutePath()); } @@ -173,9 +187,11 @@ public void runCombineGVCFSandAssertSomething(List inputs, File expected, Utils.resetRandomGenerator(); runCommandLine(args); - final List expectedVC = getVariantContexts(expected); - final List actualVC = getVariantContexts(output); - assertForEachElementInLists(actualVC, expectedVC, assertion); + if (!UPDATE_EXACT_MATCH_EXPECTED_OUTPUTS) { + final List expectedVC = getVariantContexts(expected); + final List actualVC = getVariantContexts(output); + assertForEachElementInLists(actualVC, expectedVC, assertion); + } } /** diff --git a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java index c37963259fd..a294bf9b2cd 100644 --- a/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java +++ b/src/test/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java @@ -30,6 +30,7 @@ import org.broadinstitute.hellbender.utils.io.IOUtils; import org.broadinstitute.hellbender.utils.read.GATKRead; import org.broadinstitute.hellbender.utils.variant.GATKVCFConstants; +import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils; import org.broadinstitute.hellbender.utils.variant.HomoSapiensConstants; import org.testng.Assert; import org.testng.annotations.DataProvider; @@ -1220,6 +1221,35 @@ public void testMaxAlternateAlleles(final String bam, final String reference, fi } } + @Test + public void testContaminatedHomVarDeletions() { + final String bam = toolsTestDir + "haplotypecaller/deletion_sample.snippet.bam"; + final String intervals = "chr3:46373452"; + + final File outputContaminatedHomVarDeletions = createTempFile("testContaminatedHomVarDeletions", ".vcf"); + + final ArgumentsBuilder args = new ArgumentsBuilder().addInput(new File(bam)) + .addReference(hg38Reference) + .addInterval(new SimpleInterval(intervals)) + .addOutput(outputContaminatedHomVarDeletions) + .addNumericArgument(IntervalArgumentCollection.INTERVAL_PADDING_LONG_NAME, 50); + runCommandLine(args); + + List vcs = VariantContextTestUtils.getVariantContexts(outputContaminatedHomVarDeletions); + + //check known homozygous deletion for correct genotype + for (final VariantContext vc : vcs) { + final Genotype gt = vc.getGenotype(0); + if (gt.hasAD()) { + final int[] ads = gt.getAD(); + final double alleleBalance = ads[1] / (ads[0] + ads[1]); + if (alleleBalance > 0.9) { + Assert.assertTrue(vc.getGenotype(0).isHomVar()); + } + } + } + } + /** * Helper method for testMaxAlternateAlleles * diff --git a/src/test/java/org/broadinstitute/hellbender/utils/genotyper/AlleleLikelihoodsUnitTest.java b/src/test/java/org/broadinstitute/hellbender/utils/genotyper/AlleleLikelihoodsUnitTest.java index 257cf85fd8e..9e62fb9847c 100644 --- a/src/test/java/org/broadinstitute/hellbender/utils/genotyper/AlleleLikelihoodsUnitTest.java +++ b/src/test/java/org/broadinstitute/hellbender/utils/genotyper/AlleleLikelihoodsUnitTest.java @@ -282,19 +282,18 @@ public void testNormalizeCapWorstLK(final String[] samples, final Allele[] allel for (int a = 0; a < numberOfAlleles; a++) newLikelihoods[s][a] = new double[sampleReadCount]; for (int r = 0; r < sampleReadCount; r++) { - double bestAltLk = Double.NEGATIVE_INFINITY; + double bestAlleleLk = Double.NEGATIVE_INFINITY; + //best likelihood can be alt OR reference for (int a = 0; a < numberOfAlleles; a++) { - if (alleles[a].isReference()) - continue; - bestAltLk = Math.max(bestAltLk, originalLikelihoods[s][a][r]); + bestAlleleLk = Math.max(bestAlleleLk, originalLikelihoods[s][a][r]); } - if (bestAltLk == Double.NEGATIVE_INFINITY) + if (bestAlleleLk == Double.NEGATIVE_INFINITY) for (int a = 0; a < numberOfAlleles; a++) { newLikelihoods[s][a][r] = originalLikelihoods[s][a][r]; } else for (int a = 0; a < numberOfAlleles; a++) { - newLikelihoods[s][a][r] = Math.max(originalLikelihoods[s][a][r], bestAltLk - 0.001); + newLikelihoods[s][a][r] = Math.max(originalLikelihoods[s][a][r], bestAlleleLk - 0.001); } } } diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/deletion_sample.snippet.bam b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/deletion_sample.snippet.bam new file mode 100644 index 00000000000..3b29596b74f Binary files /dev/null and b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/deletion_sample.snippet.bam differ diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/deletion_sample.snippet.bam.bai b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/deletion_sample.snippet.bam.bai new file mode 100644 index 00000000000..3681e27965c Binary files /dev/null and b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/deletion_sample.snippet.bam.bai differ diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf index cecff761f37..6eb29e368cc 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf @@ -279,10 +279,10 @@ 20 10008922 . A . . END=10008942 GT:DP:GQ:MIN_DP:PL 0/0:53:99:47:0,114,1710 20 10008943 . A . . END=10008944 GT:DP:GQ:MIN_DP:PL 0/0:47:78:47:0,78,1170 20 10008945 . A . . END=10008947 GT:DP:GQ:MIN_DP:PL 0/0:47:81:46:0,81,1215 -20 10008948 . TA T, 2081.03 . AS_RAW_BaseQRankSum=|0.9,1|NaN;AS_RAW_MQ=625.00|134397.00|0.00;AS_RAW_MQRankSum=|2.0,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=1,0|35,15|0,0;BaseQRankSum=0.994;DP=52;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=2.047;RAW_MQandDP=138622,52;ReadPosRankSum=0.884 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:1,50,0:51:99:0|1:10008921_C_CA:2095,107,0,2098,159,2150:10008921:1,0,35,15 +20 10008948 . TA T, 2091.03 . AS_RAW_BaseQRankSum=|0.9,1|NaN;AS_RAW_MQ=625.00|134397.00|0.00;AS_RAW_MQRankSum=|2.0,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=1,0|35,15|0,0;BaseQRankSum=0.994;DP=52;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=2.047;RAW_MQandDP=138622,52;ReadPosRankSum=0.884 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:1,50,0:51:99:0|1:10008921_C_CA:2105,117,0,2108,159,2150:10008921:1,0,35,15 20 10008950 . A . . END=10008950 GT:DP:GQ:MIN_DP:PL 0/0:52:99:52:0,99,1485 20 10008951 . A . . END=10008951 GT:DP:GQ:MIN_DP:PL 0/0:51:93:51:0,93,1395 -20 10008952 . CACACACACACACA C,CCA,CCACACACACA,CCACACACACACA, 1687.10 . AS_RAW_BaseQRankSum=|0.3,1|0.3,1|0.6,1|1.9,1|NaN;AS_RAW_MQ=625.00|2523.00|11774.00|12125.00|39600.00|0.00;AS_RAW_MQRankSum=|1.1,1|4.0,1|0.6,1|3.6,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|1.0,1|-0.3,1|0.8,1|NaN;AS_SB_TABLE=1,0|2,1|8,6|4,1|11,0|0,0;BaseQRankSum=0.941;DP=59;ExcessHet=3.0103;MLEAC=0,1,0,1,0;MLEAF=0.00,0.500,0.00,0.500,0.00;MQRankSum=1.844;RAW_MQandDP=154068,59;ReadPosRankSum=0.716 GT:AD:DP:GQ:PL:SB 2/4:1,3,14,5,11,0:34:99:1704,876,1258,525,811,845,726,514,173,703,582,342,0,443,530,1135,1092,744,779,607,1321:1,0,25,8 +20 10008952 . CACACACACACACA C,CCA,CCACACACACA,CCACACACACACA, 1700.10 . AS_RAW_BaseQRankSum=|0.3,1|0.3,1|0.6,1|1.9,1|NaN;AS_RAW_MQ=625.00|2523.00|11774.00|12125.00|39600.00|0.00;AS_RAW_MQRankSum=|1.1,1|4.0,1|0.6,1|3.6,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|1.0,1|-0.3,1|0.8,1|NaN;AS_SB_TABLE=1,0|2,1|8,6|4,1|11,0|0,0;BaseQRankSum=0.941;DP=59;ExcessHet=3.0103;MLEAC=0,1,0,1,0;MLEAF=0.00,0.500,0.00,0.500,0.00;MQRankSum=1.844;RAW_MQandDP=154068,59;ReadPosRankSum=0.716 GT:AD:DP:GQ:PL:SB 2/4:1,3,14,5,11,0:34:99:1717,890,1216,539,769,803,739,496,154,687,596,342,0,443,533,1149,1060,712,761,607,1292:1,0,25,8 20 10008966 . C . . END=10008986 GT:DP:GQ:MIN_DP:PL 0/0:58:99:56:0,120,1800 20 10008987 . A . . END=10008989 GT:DP:GQ:MIN_DP:PL 0/0:59:94:59:0,94,2181 20 10008990 . C . . END=10009226 GT:DP:GQ:MIN_DP:PL 0/0:61:99:38:0,102,1530 @@ -730,11 +730,11 @@ 20 10026358 . A . . END=10026793 GT:DP:GQ:MIN_DP:PL 0/0:72:99:41:0,102,1530 20 10026794 . C T, 1105.60 . AS_RAW_BaseQRankSum=|2.8,1|NaN;AS_RAW_MQ=68400.00|116041.00|0.00;AS_RAW_MQRankSum=|-0.8,1|NaN;AS_RAW_ReadPosRankSum=|-0.6,1|NaN;AS_SB_TABLE=7,12|15,18|0,0;BaseQRankSum=2.828;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.719;RAW_MQandDP=184441,52;ReadPosRankSum=-0.533 GT:AD:DP:GQ:PL:SB 0/1:19,33,0:52:99:1113,0,529,1170,627,1798:7,12,15,18 20 10026795 . G . . END=10027233 GT:DP:GQ:MIN_DP:PL 0/0:70:99:52:0,115,1800 -20 10027234 . A ATTAG, 1350.64 . AS_RAW_BaseQRankSum=|-0.5,1|NaN;AS_RAW_MQ=119641.00|106210.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|-1.0,1|NaN;AS_SB_TABLE=18,16|15,20|0,0;BaseQRankSum=-0.406;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.845;RAW_MQandDP=236651,72;ReadPosRankSum=-0.979 GT:AD:DP:GQ:PL:SB 0/1:34,35,0:69:99:1358,0,1964,1461,2069,3531:18,16,15,20 +20 10027234 . A ATTAG, 1350.64 . AS_RAW_BaseQRankSum=|-0.5,1|NaN;AS_RAW_MQ=119641.00|106210.00|0.00;AS_RAW_MQRankSum=|-0.9,1|NaN;AS_RAW_ReadPosRankSum=|-1.0,1|NaN;AS_SB_TABLE=18,16|15,20|0,0;BaseQRankSum=-0.406;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.845;RAW_MQandDP=236651,72;ReadPosRankSum=-0.979 GT:AD:DP:GQ:PL:SB 0/1:34,35,0:69:99:1358,0,1320,1461,1426,2887:18,16,15,20 20 10027235 . T . . END=10027867 GT:DP:GQ:MIN_DP:PL 0/0:78:99:56:0,120,1800 -20 10027868 . A G, 1760.60 . AS_RAW_BaseQRankSum=|-5.8,1|NaN;AS_RAW_MQ=155641.00|159241.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.8,1|NaN;AS_SB_TABLE=19,25|26,19|0,0;BaseQRankSum=-5.793;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.032;RAW_MQandDP=314882,89;ReadPosRankSum=1.872 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:44,45,0:89:99:0|1:10027868_A_G:1768,0,3201,1901,3340,5240:10027868:19,25,26,19 +20 10027868 . A G, 1760.60 . AS_RAW_BaseQRankSum=|-5.8,1|NaN;AS_RAW_MQ=155641.00|159241.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|1.8,1|NaN;AS_SB_TABLE=19,25|26,19|0,0;BaseQRankSum=-5.793;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.032;RAW_MQandDP=314882,89;ReadPosRankSum=1.872 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:44,45,0:89:99:0|1:10027868_A_G:1768,0,1671,1901,1810,3710:10027868:19,25,26,19 20 10027869 . A . . END=10027871 GT:DP:GQ:MIN_DP:PL 0/0:86:99:85:0,120,1800 -20 10027872 . A G, 1745.60 . AS_RAW_BaseQRankSum=|-5.5,1|NaN;AS_RAW_MQ=141241.00|159241.00|0.00;AS_RAW_MQRankSum=|0.1,1|NaN;AS_RAW_ReadPosRankSum=|1.0,1|NaN;AS_SB_TABLE=16,24|26,19|0,0;BaseQRankSum=-5.491;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.101;RAW_MQandDP=300482,85;ReadPosRankSum=1.053 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:40,45,0:85:99:0|1:10027868_A_G:1753,0,3136,1879,3272,5151:10027868:16,24,26,19 +20 10027872 . A G, 1745.60 . AS_RAW_BaseQRankSum=|-5.5,1|NaN;AS_RAW_MQ=141241.00|159241.00|0.00;AS_RAW_MQRankSum=|0.1,1|NaN;AS_RAW_ReadPosRankSum=|1.0,1|NaN;AS_SB_TABLE=16,24|26,19|0,0;BaseQRankSum=-5.491;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.101;RAW_MQandDP=300482,85;ReadPosRankSum=1.053 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:40,45,0:85:99:0|1:10027868_A_G:1753,0,1606,1879,1742,3621:10027868:16,24,26,19 20 10027873 . G . . END=10028866 GT:DP:GQ:MIN_DP:PL 0/0:80:99:55:0,120,1800 20 10028867 . A ATG, 1136.64 . AS_RAW_BaseQRankSum=|-0.9,1|NaN;AS_RAW_MQ=115200.00|150800.00|0.00;AS_RAW_MQRankSum=|2.7,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=11,21|18,21|0,0;BaseQRankSum=-0.874;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.711;RAW_MQandDP=338841,92;ReadPosRankSum=0.364 GT:AD:DP:GQ:PL:SB 0/1:32,39,0:71:99:1144,0,916,1242,1033,2275:11,21,18,21 20 10028868 . T . . END=10030187 GT:DP:GQ:MIN_DP:PL 0/0:80:99:60:0,120,1800 @@ -756,7 +756,7 @@ 20 10032414 . T . . END=10032881 GT:DP:GQ:MIN_DP:PL 0/0:70:99:55:0,120,1800 20 10032882 . A T, 1223.60 . AS_RAW_BaseQRankSum=|-3.7,1|NaN;AS_RAW_MQ=140400.00|126841.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|0.6,1|NaN;AS_SB_TABLE=28,11|22,14|0,0;BaseQRankSum=-3.697;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.014;RAW_MQandDP=267241,75;ReadPosRankSum=0.626 GT:AD:DP:GQ:PL:SB 0/1:39,36,0:75:99:1231,0,1406,1348,1514,2862:28,11,22,14 20 10032883 . A . . END=10032971 GT:DP:GQ:MIN_DP:PL 0/0:67:99:61:0,120,1800 -20 10032972 . C CAT, 1152.64 . AS_RAW_BaseQRankSum=|-0.4,1|NaN;AS_RAW_MQ=118800.00|105241.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|NaN;AS_SB_TABLE=17,16|11,19|0,0;BaseQRankSum=-0.354;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.017;RAW_MQandDP=231241,65;ReadPosRankSum=-1.232 GT:AD:DP:GQ:PL:SB 0/1:33,30,0:63:99:1160,0,1477,1260,1568,2827:17,16,11,19 +20 10032972 . C CAT, 1152.64 . AS_RAW_BaseQRankSum=|-0.4,1|NaN;AS_RAW_MQ=118800.00|105241.00|0.00;AS_RAW_MQRankSum=|-1.1,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|NaN;AS_SB_TABLE=17,16|11,19|0,0;BaseQRankSum=-0.354;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.017;RAW_MQandDP=231241,65;ReadPosRankSum=-1.232 GT:AD:DP:GQ:PL:SB 0/1:33,30,0:63:99:1160,0,1295,1260,1386,2645:17,16,11,19 20 10032973 . T . . END=10033636 GT:DP:GQ:MIN_DP:PL 0/0:78:99:50:0,120,1800 20 10033637 . C . . END=10033637 GT:DP:GQ:MIN_DP:PL 0/0:58:97:58:0,97,2210 20 10033638 . C . . END=10034305 GT:DP:GQ:MIN_DP:PL 0/0:85:99:53:0,120,1800 @@ -774,7 +774,7 @@ 20 10036158 . T . . END=10036160 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,117,1755 20 10036161 . T . . END=10036161 GT:DP:GQ:MIN_DP:PL 0/0:42:82:42:0,82,1514 20 10036162 . G . . END=10036929 GT:DP:GQ:MIN_DP:PL 0/0:76:99:43:0,113,1513 -20 10036930 . CGATAGCCCTAGCCCTAGATA C, 1066.60 . AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=140400.00|58242.00|0.00;AS_RAW_MQRankSum=|-4.1,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=11,28|15,14|0,0;BaseQRankSum=0.200;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.048;RAW_MQandDP=274847,93;ReadPosRankSum=0.460 GT:AD:DP:GQ:PL:SB 0/1:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 +20 10036930 . CGATAGCCCTAGCCCTAGATA C, 1066.60 . AS_RAW_BaseQRankSum=|0.2,1|NaN;AS_RAW_MQ=140400.00|58242.00|0.00;AS_RAW_MQRankSum=|-4.1,1|NaN;AS_RAW_ReadPosRankSum=|0.4,1|NaN;AS_SB_TABLE=11,28|15,14|0,0;BaseQRankSum=0.200;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.048;RAW_MQandDP=274847,93;ReadPosRankSum=0.460 GT:AD:DP:GQ:PL:SB 0/1:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 20 10036951 . G . . END=10036956 GT:DP:GQ:MIN_DP:PL 0/0:74:99:70:0,120,1800 20 10036957 . C . . END=10036957 GT:DP:GQ:MIN_DP:PL 0/0:70:37:70:0,37,2472 20 10036958 . C . . END=10036958 GT:DP:GQ:MIN_DP:PL 0/0:70:40:70:0,40,2490 @@ -829,7 +829,7 @@ 20 10042762 . G . . END=10042828 GT:DP:GQ:MIN_DP:PL 0/0:90:99:78:0,120,1800 20 10042829 . A G, 3070.03 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|278569.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|42,36|0,0;DP=78;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=278569,78 GT:AD:DP:GQ:PL:SB 1/1:0,78,0:78:99:3084,235,0,3084,235,3084:0,0,42,36 20 10042830 . C . . END=10043001 GT:DP:GQ:MIN_DP:PL 0/0:65:99:56:0,120,1800 -20 10043002 . A T, 1308.60 . AS_RAW_BaseQRankSum=|3.9,1|NaN;AS_RAW_MQ=172800.00|136800.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=19,29|18,20|0,0;BaseQRankSum=3.986;DP=86;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=309600,86;ReadPosRankSum=-0.035 GT:AD:DP:GQ:PL:SB 0/1:48,38,0:86:99:1316,0,1659,1460,1773,3233:19,29,18,20 +20 10043002 . A T, 1308.60 . AS_RAW_BaseQRankSum=|3.9,1|NaN;AS_RAW_MQ=172800.00|136800.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=19,29|18,20|0,0;BaseQRankSum=3.986;DP=86;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=309600,86;ReadPosRankSum=-0.035 GT:AD:DP:GQ:PL:SB 0/1:48,38,0:86:99:1316,0,1658,1460,1772,3232:19,29,18,20 20 10043003 . C . . END=10044848 GT:DP:GQ:MIN_DP:PL 0/0:78:99:44:0,104,1655 20 10044849 . A G, 2106.03 . AS_RAW_BaseQRankSum=||;AS_RAW_MQ=0.00|209641.00|0.00;AS_RAW_MQRankSum=||;AS_RAW_ReadPosRankSum=||;AS_SB_TABLE=0,0|22,37|0,0;DP=59;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=209641,59 GT:AD:DP:GQ:PL:SB 1/1:0,59,0:59:99:2120,177,0,2120,177,2120:0,0,22,37 20 10044850 . C . . END=10045077 GT:DP:GQ:MIN_DP:PL 0/0:69:99:56:0,120,1800 @@ -1005,9 +1005,9 @@ 20 10076400 . G . . END=10076988 GT:DP:GQ:MIN_DP:PL 0/0:73:99:51:0,120,1800 20 10076989 . CAA C,CA,CAAA, 235.10 . AS_RAW_BaseQRankSum=|-0.4,1|-1.0,1|0.1,1|NaN;AS_RAW_MQ=25200.00|10800.00|46800.00|22441.00|0.00;AS_RAW_MQRankSum=|0.0,1|0.0,1|-0.7,1|NaN;AS_RAW_ReadPosRankSum=|-1.3,1|-0.8,1|-0.4,1|NaN;AS_SB_TABLE=4,3|1,2|6,7|5,2|0,0;BaseQRankSum=-0.625;DP=75;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.473;RAW_MQandDP=253446,75;ReadPosRankSum=-0.918 GT:AD:DP:GQ:PL:SB 2/3:7,3,13,7,0:30:41:252,271,1146,41,448,376,147,276,0,361,322,712,423,318,705:4,3,12,11 20 10076992 . A . . END=10077007 GT:DP:GQ:MIN_DP:PL 0/0:69:99:59:0,120,1800 -20 10077008 . T A, 0 . AS_RAW_BaseQRankSum=|-1.9,1|NaN;AS_RAW_MQ=160082.00|11641.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=18,28|4,0|0,0;BaseQRankSum=-1.806;DP=51;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.608;RAW_MQandDP=175323,51;ReadPosRankSum=0.805 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:46,4,0:50:42:0|1:10077008_T_A:0,42,2066,148,2078,2184:10077008:18,28,4,0 +20 10077008 . T A, 0 . AS_RAW_BaseQRankSum=|-1.9,1|NaN;AS_RAW_MQ=160082.00|11641.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.8,1|NaN;AS_SB_TABLE=18,28|4,0|0,0;BaseQRankSum=-1.806;DP=51;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.608;RAW_MQandDP=175323,51;ReadPosRankSum=0.805 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:46,4,0:50:42:0|1:10077008_T_A:0,42,1971,148,1983,2089:10077008:18,28,4,0 20 10077009 . A . . END=10077009 GT:DP:GQ:MIN_DP:PL 0/0:52:99:52:0,120,1800 -20 10077010 . G A, 0 . AS_RAW_BaseQRankSum=|-1.9,1|NaN;AS_RAW_MQ=167282.00|11641.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.9,1|NaN;AS_SB_TABLE=18,30|4,0|0,0;BaseQRankSum=-1.841;DP=53;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.658;RAW_MQandDP=182523,53;ReadPosRankSum=0.911 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:48,4,0:52:42:0|1:10077008_T_A:0,42,2066,148,2078,2184:10077008:18,30,4,0 +20 10077010 . G A, 0 . AS_RAW_BaseQRankSum=|-1.9,1|NaN;AS_RAW_MQ=167282.00|11641.00|0.00;AS_RAW_MQRankSum=|-1.7,1|NaN;AS_RAW_ReadPosRankSum=|0.9,1|NaN;AS_SB_TABLE=18,30|4,0|0,0;BaseQRankSum=-1.841;DP=53;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.658;RAW_MQandDP=182523,53;ReadPosRankSum=0.911 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:48,4,0:52:42:0|1:10077008_T_A:0,42,1971,148,1983,2089:10077008:18,30,4,0 20 10077011 . A . . END=10077751 GT:DP:GQ:MIN_DP:PL 0/0:69:99:44:0,102,1654 20 10077752 . T C, 1366.60 . AS_RAW_BaseQRankSum=|-6.6,1|NaN;AS_RAW_MQ=122400.00|162000.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.4,1|NaN;AS_SB_TABLE=16,18|16,29|0,0;BaseQRankSum=-6.503;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=284400,79;ReadPosRankSum=-0.352 GT:AD:DP:GQ:PL:SB 0/1:34,45,0:79:99:1374,0,1187,1477,1322,2799:16,18,16,29 20 10077753 . G . . END=10079475 GT:DP:GQ:MIN_DP:PL 0/0:70:99:46:0,108,1620 @@ -1091,11 +1091,11 @@ 20 10088871 . T . . END=10088894 GT:DP:GQ:MIN_DP:PL 0/0:39:99:33:0,99,1294 20 10088895 . C T, 553.60 . AS_RAW_BaseQRankSum=|2.4,1|NaN;AS_RAW_MQ=74073.00|60377.00|0.00;AS_RAW_MQRankSum=|0.5,1|NaN;AS_RAW_ReadPosRankSum=|1.3,1|NaN;AS_SB_TABLE=10,13|8,10|0,0;BaseQRankSum=2.462;DP=41;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.577;RAW_MQandDP=134450,41;ReadPosRankSum=1.301 GT:AD:DP:GQ:PL:SB 0/1:23,18,0:41:99:561,0,673,630,726,1356:10,13,8,10 20 10088896 . G . . END=10088967 GT:DP:GQ:MIN_DP:PL 0/0:49:99:42:0,110,1709 -20 10088968 . C CAAA, 1205.64 . AS_RAW_BaseQRankSum=|0.5,1|NaN;AS_RAW_MQ=105241.00|42471.00|0.00;AS_RAW_MQRankSum=|-4.8,1|NaN;AS_RAW_ReadPosRankSum=|2.4,1|NaN;AS_SB_TABLE=16,14|14,9|0,0;BaseQRankSum=0.552;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.750;RAW_MQandDP=177808,62;ReadPosRankSum=2.416 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:30,23,0:53:99:0|1:10088968_C_CAAA:1213,0,1367,1310,1463,2773:10088968:16,14,14,9 +20 10088968 . C CAAA, 1205.64 . AS_RAW_BaseQRankSum=|0.5,1|NaN;AS_RAW_MQ=105241.00|42471.00|0.00;AS_RAW_MQRankSum=|-4.8,1|NaN;AS_RAW_ReadPosRankSum=|2.4,1|NaN;AS_SB_TABLE=16,14|14,9|0,0;BaseQRankSum=0.552;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.750;RAW_MQandDP=177808,62;ReadPosRankSum=2.416 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:30,23,0:53:99:0|1:10088968_C_CAAA:1213,0,1236,1310,1333,2642:10088968:16,14,14,9 20 10088969 . A . . END=10088979 GT:DP:GQ:MIN_DP:PL 0/0:71:99:70:0,120,1800 -20 10088980 . T C, 1268.60 . AS_RAW_BaseQRankSum=|-1.6,1|NaN;AS_RAW_MQ=124923.00|51430.00|0.00;AS_RAW_MQRankSum=|-5.3,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=19,18|15,16|0,0;BaseQRankSum=-1.585;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.232;RAW_MQandDP=176353,68;ReadPosRankSum=1.288 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:37,31,0:68:99:0|1:10088968_C_CAAA:1276,0,1627,1394,1729,3123:10088968:19,18,15,16 +20 10088980 . T C, 1268.60 . AS_RAW_BaseQRankSum=|-1.6,1|NaN;AS_RAW_MQ=124923.00|51430.00|0.00;AS_RAW_MQRankSum=|-5.3,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=19,18|15,16|0,0;BaseQRankSum=-1.585;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.232;RAW_MQandDP=176353,68;ReadPosRankSum=1.288 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:37,31,0:68:99:0|1:10088968_C_CAAA:1276,0,1497,1394,1599,2993:10088968:19,18,15,16 20 10088981 . A . . END=10088984 GT:DP:GQ:MIN_DP:PL 0/0:71:99:69:0,120,1800 -20 10088985 . T C, 1199.60 . AS_RAW_BaseQRankSum=|-0.2,1|NaN;AS_RAW_MQ=138965.00|52799.00|0.00;AS_RAW_MQRankSum=|-5.3,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=22,20|15,17|0,0;BaseQRankSum=-0.192;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.248;RAW_MQandDP=191764,74;ReadPosRankSum=1.228 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:42,32,0:74:99:0|1:10088968_C_CAAA:1207,0,1729,1333,1826,3159:10088968:22,20,15,17 +20 10088985 . T C, 1199.60 . AS_RAW_BaseQRankSum=|-0.2,1|NaN;AS_RAW_MQ=138965.00|52799.00|0.00;AS_RAW_MQRankSum=|-5.3,1|NaN;AS_RAW_ReadPosRankSum=|1.2,1|NaN;AS_SB_TABLE=22,20|15,17|0,0;BaseQRankSum=-0.192;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.248;RAW_MQandDP=191764,74;ReadPosRankSum=1.228 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:42,32,0:74:99:0|1:10088968_C_CAAA:1207,0,1599,1333,1695,3029:10088968:22,20,15,17 20 10088986 . A . . END=10088989 GT:DP:GQ:MIN_DP:PL 0/0:82:99:81:0,120,1800 20 10088990 . A . . END=10088990 GT:DP:GQ:MIN_DP:PL 0/0:84:7:84:0,7,2771 20 10088991 . C . . END=10088991 GT:DP:GQ:MIN_DP:PL 0/0:81:95:81:0,95,2703 @@ -1121,7 +1121,7 @@ 20 10090971 . C . . END=10091213 GT:DP:GQ:MIN_DP:PL 0/0:61:99:49:0,120,1800 20 10091214 . C T, 1270.60 . AS_RAW_BaseQRankSum=|0.3,1|NaN;AS_RAW_MQ=118800.00|130969.00|0.00;AS_RAW_MQRankSum=|-1.0,1|NaN;AS_RAW_ReadPosRankSum=|-0.1,1|NaN;AS_SB_TABLE=11,22|13,24|0,0;BaseQRankSum=0.361;DP=70;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.916;RAW_MQandDP=249769,70;ReadPosRankSum=-0.035 GT:AD:DP:GQ:PL:SB 0/1:33,37,0:70:99:1278,0,1110,1377,1222,2599:11,22,13,24 20 10091215 . C . . END=10092414 GT:DP:GQ:MIN_DP:PL 0/0:69:99:46:0,120,1800 -20 10092415 . A G, 1656.60 . AS_RAW_BaseQRankSum=|-6.8,1|NaN;AS_RAW_MQ=187200.00|176400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=27,25|24,25|0,0;BaseQRankSum=-6.731;DP=101;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=363600,101;ReadPosRankSum=0.082 GT:AD:DP:GQ:PL:SB 0/1:52,49,0:101:99:1664,0,1902,1820,2049,3870:27,25,24,25 +20 10092415 . A G, 1656.60 . AS_RAW_BaseQRankSum=|-6.8,1|NaN;AS_RAW_MQ=187200.00|176400.00|0.00;AS_RAW_MQRankSum=|0.0,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=27,25|24,25|0,0;BaseQRankSum=-6.731;DP=101;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=363600,101;ReadPosRankSum=0.082 GT:AD:DP:GQ:PL:SB 0/1:52,49,0:101:99:1664,0,1901,1820,2049,3869:27,25,24,25 20 10092416 . G . . END=10092926 GT:DP:GQ:MIN_DP:PL 0/0:80:99:60:0,120,1800 20 10092927 . G T, 127.60 . AS_RAW_BaseQRankSum=|-2.6,1|NaN;AS_RAW_MQ=212400.00|41282.00|0.00;AS_RAW_MQRankSum=|-3.1,1|NaN;AS_RAW_ReadPosRankSum=|-0.3,1|NaN;AS_SB_TABLE=43,16|0,13|0,0;BaseQRankSum=-2.507;DP=73;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.009;RAW_MQandDP=257282,73;ReadPosRankSum=-0.220 GT:AD:DP:GQ:PL:SB 0/1:59,13,0:72:99:135,0,1864,310,1901,2211:43,16,0,13 20 10092928 . T . . END=10093567 GT:DP:GQ:MIN_DP:PL 0/0:79:99:57:0,120,1800 @@ -1135,7 +1135,7 @@ 20 10094583 . T . . END=10094773 GT:DP:GQ:MIN_DP:PL 0/0:78:99:67:0,120,1800 20 10094774 . C T, 1057.60 . AS_RAW_BaseQRankSum=|-0.8,1|NaN;AS_RAW_MQ=141241.00|126000.00|0.00;AS_RAW_MQRankSum=|0.9,1|NaN;AS_RAW_ReadPosRankSum=|0.1,1|NaN;AS_SB_TABLE=24,16|21,14|0,0;BaseQRankSum=-0.784;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.962;RAW_MQandDP=267241,75;ReadPosRankSum=0.197 GT:AD:DP:GQ:PL:SB 0/1:40,35,0:75:99:1065,0,1282,1185,1385,2570:24,16,21,14 20 10094775 . A . . END=10095431 GT:DP:GQ:MIN_DP:PL 0/0:77:99:63:0,120,1800 -20 10095432 . GTGATGATGA G, 869.60 . AS_RAW_BaseQRankSum=|1.2,1|NaN;AS_RAW_MQ=97200.00|35579.00|0.00;AS_RAW_MQRankSum=|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=16,11|12,11|0,0;BaseQRankSum=1.265;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.431;RAW_MQandDP=227748,77;ReadPosRankSum=0.396 GT:AD:DP:GQ:PL:SB 0/1:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11 +20 10095432 . GTGATGATGA G, 869.60 . AS_RAW_BaseQRankSum=|1.2,1|NaN;AS_RAW_MQ=97200.00|35579.00|0.00;AS_RAW_MQRankSum=|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|0.3,1|NaN;AS_SB_TABLE=16,11|12,11|0,0;BaseQRankSum=1.265;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.431;RAW_MQandDP=227748,77;ReadPosRankSum=0.396 GT:AD:DP:GQ:PL:SB 0/1:27,23,0:50:99:877,0,998,959,1071,2030:16,11,12,11 20 10095442 . T . . END=10095740 GT:DP:GQ:MIN_DP:PL 0/0:80:99:64:0,120,1800 20 10095741 . A G, 1096.60 . AS_RAW_BaseQRankSum=|-0.6,1|NaN;AS_RAW_MQ=126841.00|103087.00|0.00;AS_RAW_MQRankSum=|-2.4,1|NaN;AS_RAW_ReadPosRankSum=|-0.5,1|NaN;AS_SB_TABLE=14,22|18,16|0,0;BaseQRankSum=-0.534;DP=71;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.313;RAW_MQandDP=233528,71;ReadPosRankSum=-0.500 GT:AD:DP:GQ:PL:SB 0/1:36,34,0:70:99:1104,0,1233,1213,1335,2547:14,22,18,16 20 10095742 . G . . END=10096292 GT:DP:GQ:MIN_DP:PL 0/0:73:99:63:0,120,1800 @@ -1155,7 +1155,7 @@ 20 10096959 . G . . END=10097074 GT:DP:GQ:MIN_DP:PL 0/0:92:99:84:0,120,1800 20 10097075 . T G, 1466.60 . AS_RAW_BaseQRankSum=|-2.6,1|NaN;AS_RAW_MQ=159700.00|155928.00|0.00;AS_RAW_MQRankSum=|-1.4,1|NaN;AS_RAW_ReadPosRankSum=|0.0,1|NaN;AS_SB_TABLE=18,26|26,22|0,0;BaseQRankSum=-2.533;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.389;RAW_MQandDP=315628,92;ReadPosRankSum=0.082 GT:AD:DP:GQ:PL:SB 0/1:44,48,0:92:99:1474,0,1482,1606,1626,3232:18,26,26,22 20 10097076 . A . . END=10097100 GT:DP:GQ:MIN_DP:PL 0/0:91:99:77:0,120,1800 -20 10097101 . C CTTT,CTTTT, 1121.64 . AS_RAW_BaseQRankSum=|-0.9,1|-1.2,1|NaN;AS_RAW_MQ=121504.00|76887.00|6803.00|0.00;AS_RAW_MQRankSum=|-1.8,1|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|2.7,1|-1.4,1|NaN;AS_SB_TABLE=22,12|12,14|3,1|0,0;BaseQRankSum=-1.134;DP=76;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=-2.428;RAW_MQandDP=252294,76;ReadPosRankSum=2.086 GT:AD:DP:GQ:PL:SB 0/1:34,26,4,0:64:99:1129,0,1306,558,1324,2012,982,1430,2052,2377:22,12,15,15 +20 10097101 . C CTTT,CTTTT, 1121.64 . AS_RAW_BaseQRankSum=|-0.9,1|-1.2,1|NaN;AS_RAW_MQ=121504.00|76887.00|6803.00|0.00;AS_RAW_MQRankSum=|-1.8,1|-4.5,1|NaN;AS_RAW_ReadPosRankSum=|2.7,1|-1.4,1|NaN;AS_SB_TABLE=22,12|12,14|3,1|0,0;BaseQRankSum=-1.134;DP=76;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=-2.428;RAW_MQandDP=252294,76;ReadPosRankSum=2.086 GT:AD:DP:GQ:PL:SB 0/1:34,26,4,0:64:99:1129,0,1259,558,1242,1826,982,1358,1910,2261:22,12,15,15 20 10097102 . T . . END=10097435 GT:DP:GQ:MIN_DP:PL 0/0:70:99:60:0,120,1800 20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C, 1084.60 . AS_RAW_BaseQRankSum=|1.8,1|NaN;AS_RAW_MQ=204882.00|57261.00|0.00;AS_RAW_MQRankSum=|-6.5,1|NaN;AS_RAW_ReadPosRankSum=|-3.1,1|NaN;AS_SB_TABLE=23,34|11,21|0,0;BaseQRankSum=1.820;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.464;RAW_MQandDP=262143,89;ReadPosRankSum=-3.097 GT:AD:DP:GQ:PL:SB 0/1:57,32,0:89:99:1092,0,2241,1263,2338,3601:23,34,11,21 20 10097437 . TTTTC *,T, 930.01 . AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=0.00|57261.00|84469.00|0.00;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=0,0|11,21|5,18|0,0;DP=76;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;RAW_MQandDP=217330,76 GT:AD:DP:GQ:PL:SB 1/2:0,32,23,0:55:99:2127,940,1799,1195,0,1125,2201,1453,1262,2642:0,0,16,39 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf.idx index a1076afd13b..19c941ba6f6 100644 Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.alleleSpecific.g.vcf.idx differ diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf index f676c388845..5124565e05d 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf @@ -272,10 +272,10 @@ 20 10008922 . A . . END=10008942 GT:DP:GQ:MIN_DP:PL 0/0:53:99:47:0,114,1710 20 10008943 . A . . END=10008944 GT:DP:GQ:MIN_DP:PL 0/0:47:78:47:0,78,1170 20 10008945 . A . . END=10008947 GT:DP:GQ:MIN_DP:PL 0/0:47:81:46:0,81,1215 -20 10008948 . TA T, 2081.03 . BaseQRankSum=0.994;DP=52;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=2.047;RAW_MQandDP=138622,52;ReadPosRankSum=0.884 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:1,50,0:51:99:0|1:10008921_C_CA:2095,107,0,2098,159,2150:10008921:1,0,35,15 +20 10008948 . TA T, 2091.03 . BaseQRankSum=0.994;DP=52;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;MQRankSum=2.047;RAW_MQandDP=138622,52;ReadPosRankSum=0.884 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 1|1:1,50,0:51:99:0|1:10008921_C_CA:2105,117,0,2108,159,2150:10008921:1,0,35,15 20 10008950 . A . . END=10008950 GT:DP:GQ:MIN_DP:PL 0/0:52:99:52:0,99,1485 20 10008951 . A . . END=10008951 GT:DP:GQ:MIN_DP:PL 0/0:51:93:51:0,93,1395 -20 10008952 . CACACACACACACA C,CCA,CCACACACACA,CCACACACACACA, 1687.10 . BaseQRankSum=0.941;DP=59;ExcessHet=3.0103;MLEAC=0,1,0,1,0;MLEAF=0.00,0.500,0.00,0.500,0.00;MQRankSum=1.844;RAW_MQandDP=154068,59;ReadPosRankSum=0.716 GT:AD:DP:GQ:PL:SB 2/4:1,3,14,5,11,0:34:99:1704,876,1258,525,811,845,726,514,173,703,582,342,0,443,530,1135,1092,744,779,607,1321:1,0,25,8 +20 10008952 . CACACACACACACA C,CCA,CCACACACACA,CCACACACACACA, 1700.10 . BaseQRankSum=0.941;DP=59;ExcessHet=3.0103;MLEAC=0,1,0,1,0;MLEAF=0.00,0.500,0.00,0.500,0.00;MQRankSum=1.844;RAW_MQandDP=154068,59;ReadPosRankSum=0.716 GT:AD:DP:GQ:PL:SB 2/4:1,3,14,5,11,0:34:99:1717,890,1216,539,769,803,739,496,154,687,596,342,0,443,533,1149,1060,712,761,607,1292:1,0,25,8 20 10008966 . C . . END=10008986 GT:DP:GQ:MIN_DP:PL 0/0:58:99:56:0,120,1800 20 10008987 . A . . END=10008989 GT:DP:GQ:MIN_DP:PL 0/0:59:94:59:0,94,2181 20 10008990 . C . . END=10009226 GT:DP:GQ:MIN_DP:PL 0/0:61:99:38:0,102,1530 @@ -723,11 +723,11 @@ 20 10026358 . A . . END=10026793 GT:DP:GQ:MIN_DP:PL 0/0:72:99:41:0,102,1530 20 10026794 . C T, 1105.60 . BaseQRankSum=2.828;DP=52;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.719;RAW_MQandDP=184441,52;ReadPosRankSum=-0.533 GT:AD:DP:GQ:PL:SB 0/1:19,33,0:52:99:1113,0,529,1170,627,1798:7,12,15,18 20 10026795 . G . . END=10027233 GT:DP:GQ:MIN_DP:PL 0/0:70:99:52:0,115,1800 -20 10027234 . A ATTAG, 1350.64 . BaseQRankSum=-0.406;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.845;RAW_MQandDP=236651,72;ReadPosRankSum=-0.979 GT:AD:DP:GQ:PL:SB 0/1:34,35,0:69:99:1358,0,1964,1461,2069,3531:18,16,15,20 +20 10027234 . A ATTAG, 1350.64 . BaseQRankSum=-0.406;DP=72;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.845;RAW_MQandDP=236651,72;ReadPosRankSum=-0.979 GT:AD:DP:GQ:PL:SB 0/1:34,35,0:69:99:1358,0,1320,1461,1426,2887:18,16,15,20 20 10027235 . T . . END=10027867 GT:DP:GQ:MIN_DP:PL 0/0:78:99:56:0,120,1800 -20 10027868 . A G, 1760.60 . BaseQRankSum=-5.793;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.032;RAW_MQandDP=314882,89;ReadPosRankSum=1.872 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:44,45,0:89:99:0|1:10027868_A_G:1768,0,3201,1901,3340,5240:10027868:19,25,26,19 +20 10027868 . A G, 1760.60 . BaseQRankSum=-5.793;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.032;RAW_MQandDP=314882,89;ReadPosRankSum=1.872 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:44,45,0:89:99:0|1:10027868_A_G:1768,0,1671,1901,1810,3710:10027868:19,25,26,19 20 10027869 . A . . END=10027871 GT:DP:GQ:MIN_DP:PL 0/0:86:99:85:0,120,1800 -20 10027872 . A G, 1745.60 . BaseQRankSum=-5.491;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.101;RAW_MQandDP=300482,85;ReadPosRankSum=1.053 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:40,45,0:85:99:0|1:10027868_A_G:1753,0,3136,1879,3272,5151:10027868:16,24,26,19 +20 10027872 . A G, 1745.60 . BaseQRankSum=-5.491;DP=85;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.101;RAW_MQandDP=300482,85;ReadPosRankSum=1.053 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:40,45,0:85:99:0|1:10027868_A_G:1753,0,1606,1879,1742,3621:10027868:16,24,26,19 20 10027873 . G . . END=10028866 GT:DP:GQ:MIN_DP:PL 0/0:80:99:55:0,120,1800 20 10028867 . A ATG, 1136.64 . BaseQRankSum=-0.874;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=2.711;RAW_MQandDP=338841,92;ReadPosRankSum=0.364 GT:AD:DP:GQ:PL:SB 0/1:32,39,0:71:99:1144,0,916,1242,1033,2275:11,21,18,21 20 10028868 . T . . END=10030187 GT:DP:GQ:MIN_DP:PL 0/0:80:99:60:0,120,1800 @@ -749,7 +749,7 @@ 20 10032414 . T . . END=10032881 GT:DP:GQ:MIN_DP:PL 0/0:70:99:55:0,120,1800 20 10032882 . A T, 1223.60 . BaseQRankSum=-3.697;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.014;RAW_MQandDP=267241,75;ReadPosRankSum=0.626 GT:AD:DP:GQ:PL:SB 0/1:39,36,0:75:99:1231,0,1406,1348,1514,2862:28,11,22,14 20 10032883 . A . . END=10032971 GT:DP:GQ:MIN_DP:PL 0/0:67:99:61:0,120,1800 -20 10032972 . C CAT, 1152.64 . BaseQRankSum=-0.354;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.017;RAW_MQandDP=231241,65;ReadPosRankSum=-1.232 GT:AD:DP:GQ:PL:SB 0/1:33,30,0:63:99:1160,0,1477,1260,1568,2827:17,16,11,19 +20 10032972 . C CAT, 1152.64 . BaseQRankSum=-0.354;DP=65;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.017;RAW_MQandDP=231241,65;ReadPosRankSum=-1.232 GT:AD:DP:GQ:PL:SB 0/1:33,30,0:63:99:1160,0,1295,1260,1386,2645:17,16,11,19 20 10032973 . T . . END=10033636 GT:DP:GQ:MIN_DP:PL 0/0:78:99:50:0,120,1800 20 10033637 . C . . END=10033637 GT:DP:GQ:MIN_DP:PL 0/0:58:97:58:0,97,2210 20 10033638 . C . . END=10034305 GT:DP:GQ:MIN_DP:PL 0/0:85:99:53:0,120,1800 @@ -767,7 +767,7 @@ 20 10036158 . T . . END=10036160 GT:DP:GQ:MIN_DP:PL 0/0:42:99:40:0,117,1755 20 10036161 . T . . END=10036161 GT:DP:GQ:MIN_DP:PL 0/0:42:82:42:0,82,1514 20 10036162 . G . . END=10036929 GT:DP:GQ:MIN_DP:PL 0/0:76:99:43:0,113,1513 -20 10036930 . CGATAGCCCTAGCCCTAGATA C, 1066.60 . BaseQRankSum=0.200;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.048;RAW_MQandDP=274847,93;ReadPosRankSum=0.460 GT:AD:DP:GQ:PL:SB 0/1:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 +20 10036930 . CGATAGCCCTAGCCCTAGATA C, 1066.60 . BaseQRankSum=0.200;DP=93;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.048;RAW_MQandDP=274847,93;ReadPosRankSum=0.460 GT:AD:DP:GQ:PL:SB 0/1:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 20 10036951 . G . . END=10036956 GT:DP:GQ:MIN_DP:PL 0/0:74:99:70:0,120,1800 20 10036957 . C . . END=10036957 GT:DP:GQ:MIN_DP:PL 0/0:70:37:70:0,37,2472 20 10036958 . C . . END=10036958 GT:DP:GQ:MIN_DP:PL 0/0:70:40:70:0,40,2490 @@ -822,7 +822,7 @@ 20 10042762 . G . . END=10042828 GT:DP:GQ:MIN_DP:PL 0/0:90:99:78:0,120,1800 20 10042829 . A G, 3070.03 . DP=78;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=278569,78 GT:AD:DP:GQ:PL:SB 1/1:0,78,0:78:99:3084,235,0,3084,235,3084:0,0,42,36 20 10042830 . C . . END=10043001 GT:DP:GQ:MIN_DP:PL 0/0:65:99:56:0,120,1800 -20 10043002 . A T, 1308.60 . BaseQRankSum=3.986;DP=86;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=309600,86;ReadPosRankSum=-0.035 GT:AD:DP:GQ:PL:SB 0/1:48,38,0:86:99:1316,0,1659,1460,1773,3233:19,29,18,20 +20 10043002 . A T, 1308.60 . BaseQRankSum=3.986;DP=86;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=309600,86;ReadPosRankSum=-0.035 GT:AD:DP:GQ:PL:SB 0/1:48,38,0:86:99:1316,0,1658,1460,1772,3232:19,29,18,20 20 10043003 . C . . END=10044848 GT:DP:GQ:MIN_DP:PL 0/0:78:99:44:0,104,1655 20 10044849 . A G, 2106.03 . DP=59;ExcessHet=3.0103;MLEAC=2,0;MLEAF=1.00,0.00;RAW_MQandDP=209641,59 GT:AD:DP:GQ:PL:SB 1/1:0,59,0:59:99:2120,177,0,2120,177,2120:0,0,22,37 20 10044850 . C . . END=10045077 GT:DP:GQ:MIN_DP:PL 0/0:69:99:56:0,120,1800 @@ -998,9 +998,9 @@ 20 10076400 . G . . END=10076988 GT:DP:GQ:MIN_DP:PL 0/0:73:99:51:0,120,1800 20 10076989 . CAA C,CA,CAAA, 235.10 . BaseQRankSum=-0.625;DP=75;ExcessHet=3.0103;MLEAC=0,1,1,0;MLEAF=0.00,0.500,0.500,0.00;MQRankSum=-0.473;RAW_MQandDP=253446,75;ReadPosRankSum=-0.918 GT:AD:DP:GQ:PL:SB 2/3:7,3,13,7,0:30:41:252,271,1146,41,448,376,147,276,0,361,322,712,423,318,705:4,3,12,11 20 10076992 . A . . END=10077007 GT:DP:GQ:MIN_DP:PL 0/0:69:99:59:0,120,1800 -20 10077008 . T A, 0 . BaseQRankSum=-1.806;DP=51;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.608;RAW_MQandDP=175323,51;ReadPosRankSum=0.805 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:46,4,0:50:42:0|1:10077008_T_A:0,42,2066,148,2078,2184:10077008:18,28,4,0 +20 10077008 . T A, 0 . BaseQRankSum=-1.806;DP=51;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.608;RAW_MQandDP=175323,51;ReadPosRankSum=0.805 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:46,4,0:50:42:0|1:10077008_T_A:0,42,1971,148,1983,2089:10077008:18,28,4,0 20 10077009 . A . . END=10077009 GT:DP:GQ:MIN_DP:PL 0/0:52:99:52:0,120,1800 -20 10077010 . G A, 0 . BaseQRankSum=-1.841;DP=53;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.658;RAW_MQandDP=182523,53;ReadPosRankSum=0.911 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:48,4,0:52:42:0|1:10077008_T_A:0,42,2066,148,2078,2184:10077008:18,30,4,0 +20 10077010 . G A, 0 . BaseQRankSum=-1.841;DP=53;ExcessHet=3.0103;MLEAC=0,0;MLEAF=0.00,0.00;MQRankSum=-1.658;RAW_MQandDP=182523,53;ReadPosRankSum=0.911 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|0:48,4,0:52:42:0|1:10077008_T_A:0,42,1971,148,1983,2089:10077008:18,30,4,0 20 10077011 . A . . END=10077751 GT:DP:GQ:MIN_DP:PL 0/0:69:99:44:0,102,1654 20 10077752 . T C, 1366.60 . BaseQRankSum=-6.503;DP=79;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=284400,79;ReadPosRankSum=-0.352 GT:AD:DP:GQ:PL:SB 0/1:34,45,0:79:99:1374,0,1187,1477,1322,2799:16,18,16,29 20 10077753 . G . . END=10079475 GT:DP:GQ:MIN_DP:PL 0/0:70:99:46:0,108,1620 @@ -1084,11 +1084,11 @@ 20 10088871 . T . . END=10088894 GT:DP:GQ:MIN_DP:PL 0/0:39:99:33:0,99,1294 20 10088895 . C T, 553.60 . BaseQRankSum=2.462;DP=41;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.577;RAW_MQandDP=134450,41;ReadPosRankSum=1.301 GT:AD:DP:GQ:PL:SB 0/1:23,18,0:41:99:561,0,673,630,726,1356:10,13,8,10 20 10088896 . G . . END=10088967 GT:DP:GQ:MIN_DP:PL 0/0:49:99:42:0,110,1709 -20 10088968 . C CAAA, 1205.64 . BaseQRankSum=0.552;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.750;RAW_MQandDP=177808,62;ReadPosRankSum=2.416 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:30,23,0:53:99:0|1:10088968_C_CAAA:1213,0,1367,1310,1463,2773:10088968:16,14,14,9 +20 10088968 . C CAAA, 1205.64 . BaseQRankSum=0.552;DP=62;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.750;RAW_MQandDP=177808,62;ReadPosRankSum=2.416 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:30,23,0:53:99:0|1:10088968_C_CAAA:1213,0,1236,1310,1333,2642:10088968:16,14,14,9 20 10088969 . A . . END=10088979 GT:DP:GQ:MIN_DP:PL 0/0:71:99:70:0,120,1800 -20 10088980 . T C, 1268.60 . BaseQRankSum=-1.585;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.232;RAW_MQandDP=176353,68;ReadPosRankSum=1.288 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:37,31,0:68:99:0|1:10088968_C_CAAA:1276,0,1627,1394,1729,3123:10088968:19,18,15,16 +20 10088980 . T C, 1268.60 . BaseQRankSum=-1.585;DP=68;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.232;RAW_MQandDP=176353,68;ReadPosRankSum=1.288 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:37,31,0:68:99:0|1:10088968_C_CAAA:1276,0,1497,1394,1599,2993:10088968:19,18,15,16 20 10088981 . A . . END=10088984 GT:DP:GQ:MIN_DP:PL 0/0:71:99:69:0,120,1800 -20 10088985 . T C, 1199.60 . BaseQRankSum=-0.192;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.248;RAW_MQandDP=191764,74;ReadPosRankSum=1.228 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:42,32,0:74:99:0|1:10088968_C_CAAA:1207,0,1729,1333,1826,3159:10088968:22,20,15,17 +20 10088985 . T C, 1199.60 . BaseQRankSum=-0.192;DP=74;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-5.248;RAW_MQandDP=191764,74;ReadPosRankSum=1.228 GT:AD:DP:GQ:PGT:PID:PL:PS:SB 0|1:42,32,0:74:99:0|1:10088968_C_CAAA:1207,0,1599,1333,1695,3029:10088968:22,20,15,17 20 10088986 . A . . END=10088989 GT:DP:GQ:MIN_DP:PL 0/0:82:99:81:0,120,1800 20 10088990 . A . . END=10088990 GT:DP:GQ:MIN_DP:PL 0/0:84:7:84:0,7,2771 20 10088991 . C . . END=10088991 GT:DP:GQ:MIN_DP:PL 0/0:81:95:81:0,95,2703 @@ -1114,7 +1114,7 @@ 20 10090971 . C . . END=10091213 GT:DP:GQ:MIN_DP:PL 0/0:61:99:49:0,120,1800 20 10091214 . C T, 1270.60 . BaseQRankSum=0.361;DP=70;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-0.916;RAW_MQandDP=249769,70;ReadPosRankSum=-0.035 GT:AD:DP:GQ:PL:SB 0/1:33,37,0:70:99:1278,0,1110,1377,1222,2599:11,22,13,24 20 10091215 . C . . END=10092414 GT:DP:GQ:MIN_DP:PL 0/0:69:99:46:0,120,1800 -20 10092415 . A G, 1656.60 . BaseQRankSum=-6.731;DP=101;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=363600,101;ReadPosRankSum=0.082 GT:AD:DP:GQ:PL:SB 0/1:52,49,0:101:99:1664,0,1902,1820,2049,3870:27,25,24,25 +20 10092415 . A G, 1656.60 . BaseQRankSum=-6.731;DP=101;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.000;RAW_MQandDP=363600,101;ReadPosRankSum=0.082 GT:AD:DP:GQ:PL:SB 0/1:52,49,0:101:99:1664,0,1901,1820,2049,3869:27,25,24,25 20 10092416 . G . . END=10092926 GT:DP:GQ:MIN_DP:PL 0/0:80:99:60:0,120,1800 20 10092927 . G T, 127.60 . BaseQRankSum=-2.507;DP=73;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-3.009;RAW_MQandDP=257282,73;ReadPosRankSum=-0.220 GT:AD:DP:GQ:PL:SB 0/1:59,13,0:72:99:135,0,1864,310,1901,2211:43,16,0,13 20 10092928 . T . . END=10093567 GT:DP:GQ:MIN_DP:PL 0/0:79:99:57:0,120,1800 @@ -1128,7 +1128,7 @@ 20 10094583 . T . . END=10094773 GT:DP:GQ:MIN_DP:PL 0/0:78:99:67:0,120,1800 20 10094774 . C T, 1057.60 . BaseQRankSum=-0.784;DP=75;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=0.962;RAW_MQandDP=267241,75;ReadPosRankSum=0.197 GT:AD:DP:GQ:PL:SB 0/1:40,35,0:75:99:1065,0,1282,1185,1385,2570:24,16,21,14 20 10094775 . A . . END=10095431 GT:DP:GQ:MIN_DP:PL 0/0:77:99:63:0,120,1800 -20 10095432 . GTGATGATGA G, 869.60 . BaseQRankSum=1.265;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.431;RAW_MQandDP=227748,77;ReadPosRankSum=0.396 GT:AD:DP:GQ:PL:SB 0/1:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11 +20 10095432 . GTGATGATGA G, 869.60 . BaseQRankSum=1.265;DP=77;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-4.431;RAW_MQandDP=227748,77;ReadPosRankSum=0.396 GT:AD:DP:GQ:PL:SB 0/1:27,23,0:50:99:877,0,998,959,1071,2030:16,11,12,11 20 10095442 . T . . END=10095740 GT:DP:GQ:MIN_DP:PL 0/0:80:99:64:0,120,1800 20 10095741 . A G, 1096.60 . BaseQRankSum=-0.534;DP=71;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-2.313;RAW_MQandDP=233528,71;ReadPosRankSum=-0.500 GT:AD:DP:GQ:PL:SB 0/1:36,34,0:70:99:1104,0,1233,1213,1335,2547:14,22,18,16 20 10095742 . G . . END=10096292 GT:DP:GQ:MIN_DP:PL 0/0:73:99:63:0,120,1800 @@ -1148,7 +1148,7 @@ 20 10096959 . G . . END=10097074 GT:DP:GQ:MIN_DP:PL 0/0:92:99:84:0,120,1800 20 10097075 . T G, 1466.60 . BaseQRankSum=-2.533;DP=92;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-1.389;RAW_MQandDP=315628,92;ReadPosRankSum=0.082 GT:AD:DP:GQ:PL:SB 0/1:44,48,0:92:99:1474,0,1482,1606,1626,3232:18,26,26,22 20 10097076 . A . . END=10097100 GT:DP:GQ:MIN_DP:PL 0/0:91:99:77:0,120,1800 -20 10097101 . C CTTT,CTTTT, 1121.64 . BaseQRankSum=-1.134;DP=76;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=-2.428;RAW_MQandDP=252294,76;ReadPosRankSum=2.086 GT:AD:DP:GQ:PL:SB 0/1:34,26,4,0:64:99:1129,0,1306,558,1324,2012,982,1430,2052,2377:22,12,15,15 +20 10097101 . C CTTT,CTTTT, 1121.64 . BaseQRankSum=-1.134;DP=76;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=-2.428;RAW_MQandDP=252294,76;ReadPosRankSum=2.086 GT:AD:DP:GQ:PL:SB 0/1:34,26,4,0:64:99:1129,0,1259,558,1242,1826,982,1358,1910,2261:22,12,15,15 20 10097102 . T . . END=10097435 GT:DP:GQ:MIN_DP:PL 0/0:70:99:60:0,120,1800 20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C, 1084.60 . BaseQRankSum=1.820;DP=89;ExcessHet=3.0103;MLEAC=1,0;MLEAF=0.500,0.00;MQRankSum=-6.464;RAW_MQandDP=262143,89;ReadPosRankSum=-3.097 GT:AD:DP:GQ:PL:SB 0/1:57,32,0:89:99:1092,0,2241,1263,2338,3601:23,34,11,21 20 10097437 . TTTTC *,T, 930.01 . DP=76;ExcessHet=3.0103;MLEAC=1,1,0;MLEAF=0.500,0.500,0.00;RAW_MQandDP=217330,76 GT:AD:DP:GQ:PL:SB 1/2:0,32,23,0:55:99:2127,940,1799,1195,0,1125,2201,1453,1262,2642:0,0,16,39 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf.idx index 3f1ba24ba54..3044033a163 100644 Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testGVCFMode.gatk4.g.vcf.idx differ diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.nonstrict.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.nonstrict.vcf index 2f4bea236c4..4dd179f62f6 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.nonstrict.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.nonstrict.vcf @@ -83,8 +83,8 @@ 20 10008742 . G T 736.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.893;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.22;MQRankSum=-1.502;QD=15.03;ReadPosRankSum=0.190;SOR=0.741 GT:AD:DP:GQ:PL 0/1:23,26:49:99:744,0,580 20 10008758 . C CA 707.53 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.130;DP=44;ExcessHet=3.0103;FS=2.160;MLEAC=1;MLEAF=0.500;MQ=35.24;MQRankSum=-1.168;QD=20.22;ReadPosRankSum=-0.052;SOR=0.249 GT:AD:DP:GQ:PL 1/1:4,31:35:10:721,10,0 20 10008921 . C CA 283.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.610;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.34;MQRankSum=-1.906;QD=8.34;ReadPosRankSum=0.173;SOR=0.512 GT:AD:DP:GQ:PL 0/1:18,16:34:99:291,0,366 -20 10008948 . TA T 2081.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.994;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.63;MQRankSum=2.047;QD=27.08;ReadPosRankSum=0.884;SOR=0.818 GT:AD:DP:GQ:PL 1/1:1,50:51:99:2095,107,0 -20 10008952 . CACACACACACA C,CCACACACACA 1687.10 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.963;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=51.10;MQRankSum=1.976;QD=25.42;ReadPosRankSum=0.934;SOR=1.112 GT:AD:DP:GQ:PL 1/2:1,17,18:36:99:1704,525,844,582,0,531 +20 10008948 . TA T 2092.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.994;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.63;MQRankSum=2.047;QD=27.08;ReadPosRankSum=0.884;SOR=0.818 GT:AD:DP:GQ:PL 1/1:1,50:51:99:2106,117,0 +20 10008952 . CACACACACACA C,CCACACACACA 1701.10 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.963;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=51.10;MQRankSum=1.976;QD=25.42;ReadPosRankSum=0.934;SOR=1.112 GT:AD:DP:GQ:PL 1/2:1,17,18:36:99:1718,539,802,596,0,534 20 10009227 . A G 1390.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.220;DP=62;ExcessHet=3.0103;FS=9.110;MLEAC=1;MLEAF=0.500;MQ=57.16;MQRankSum=1.428;QD=22.43;ReadPosRankSum=-1.159;SOR=0.281 GT:AD:DP:GQ:PL 0/1:23,39:62:99:1398,0,740 20 10009246 . A G 3017.03 . AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.09;QD=27.65;SOR=0.887 GT:AD:DP:GQ:PL 1/1:0,77:77:99:3031,231,0 20 10009400 . T A 3013.03 . AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.48;SOR=0.804 GT:AD:DP:GQ:PL 1/1:0,74:74:99:3027,223,0 @@ -134,9 +134,9 @@ 20 10024300 . C CTT 104.67 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.362;DP=50;ExcessHet=3.0103;FS=3.090;MLEAC=1;MLEAF=0.500;MQ=51.90;MQRankSum=-0.084;QD=6.16;ReadPosRankSum=-0.431;SOR=1.773 GT:AD:DP:GQ:PL 0/1:9,8:17:99:103,0,137 20 10026357 . T C 1187.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.700;DP=63;ExcessHet=3.0103;FS=8.911;MLEAC=1;MLEAF=0.500;MQ=58.43;MQRankSum=-0.148;QD=18.85;ReadPosRankSum=-0.076;SOR=0.722 GT:AD:DP:GQ:PL 0/1:28,35:63:99:1195,0,932 20 10026794 . C T 1105.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.828;DP=52;ExcessHet=3.0103;FS=2.399;MLEAC=1;MLEAF=0.500;MQ=59.56;MQRankSum=-0.719;QD=21.26;ReadPosRankSum=-0.533;SOR=0.428 GT:AD:DP:GQ:PL 0/1:19,33:52:99:1113,0,529 -20 10027234 . A ATTAG 1350.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.406;DP=72;ExcessHet=3.0103;FS=3.248;MLEAC=1;MLEAF=0.500;MQ=57.33;MQRankSum=-0.845;QD=19.57;ReadPosRankSum=-0.979;SOR=0.926 GT:AD:DP:GQ:PL 0/1:34,35:69:99:1358,0,1964 -20 10027868 . A G 1760.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-5.793;DP=89;ExcessHet=3.0103;FS=6.868;MLEAC=1;MLEAF=0.500;MQ=59.48;MQRankSum=0.032;QD=19.78;ReadPosRankSum=1.872;SOR=0.881 GT:AD:DP:GQ:PL 0/1:44,45:89:99:1768,0,3201 -20 10027872 . A G 1745.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-5.491;DP=85;ExcessHet=3.0103;FS=8.870;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=0.101;QD=20.54;ReadPosRankSum=1.053;SOR=0.826 GT:AD:DP:GQ:PL 0/1:40,45:85:99:1753,0,3136 +20 10027234 . A ATTAG 1350.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.406;DP=72;ExcessHet=3.0103;FS=3.248;MLEAC=1;MLEAF=0.500;MQ=57.33;MQRankSum=-0.845;QD=19.57;ReadPosRankSum=-0.979;SOR=0.926 GT:AD:DP:GQ:PL 0/1:34,35:69:99:1358,0,1320 +20 10027868 . A G 1760.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-5.793;DP=89;ExcessHet=3.0103;FS=6.868;MLEAC=1;MLEAF=0.500;MQ=59.48;MQRankSum=0.032;QD=19.78;ReadPosRankSum=1.872;SOR=0.881 GT:AD:DP:GQ:PL 0/1:44,45:89:99:1768,0,1671 +20 10027872 . A G 1745.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-5.491;DP=85;ExcessHet=3.0103;FS=8.870;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=0.101;QD=20.54;ReadPosRankSum=1.053;SOR=0.826 GT:AD:DP:GQ:PL 0/1:40,45:85:99:1753,0,1606 20 10028867 . A ATG 1136.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.874;DP=92;ExcessHet=3.0103;FS=4.652;MLEAC=1;MLEAF=0.500;MQ=60.69;MQRankSum=2.711;QD=16.01;ReadPosRankSum=0.364;SOR=0.336 GT:AD:DP:GQ:PL 0/1:32,39:71:99:1144,0,916 20 10030188 . T A 1393.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.711;DP=81;ExcessHet=3.0103;FS=9.186;MLEAC=1;MLEAF=0.500;MQ=59.72;MQRankSum=-1.013;QD=17.20;ReadPosRankSum=-0.553;SOR=1.105 GT:AD:DP:GQ:PL 0/1:42,39:81:99:1401,0,1524 20 10031254 . A AT 1493.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.091;DP=86;ExcessHet=3.0103;FS=9.250;MLEAC=1;MLEAF=0.500;MQ=59.91;MQRankSum=0.017;QD=17.57;ReadPosRankSum=0.495;SOR=0.211 GT:AD:DP:GQ:PL 0/1:38,47:85:99:1501,0,1159 @@ -146,9 +146,9 @@ 20 10032094 . G A 1241.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=5.488;DP=83;ExcessHet=3.0103;FS=6.039;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=14.96;ReadPosRankSum=-0.579;SOR=0.260 GT:AD:DP:GQ:PL 0/1:47,36:83:99:1249,0,1497 20 10032413 . T G 890.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-6.142;DP=66;ExcessHet=3.0103;FS=10.444;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=-0.065;QD=13.49;ReadPosRankSum=-1.003;SOR=1.293 GT:AD:DP:GQ:PL 0/1:35,31:66:99:898,0,1277 20 10032882 . A T 1223.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.697;DP=75;ExcessHet=3.0103;FS=4.673;MLEAC=1;MLEAF=0.500;MQ=59.69;MQRankSum=-1.014;QD=16.31;ReadPosRankSum=0.626;SOR=0.338 GT:AD:DP:GQ:PL 0/1:39,36:75:99:1231,0,1406 -20 10032972 . C CAT 1152.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.354;DP=65;ExcessHet=3.0103;FS=5.062;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=-1.017;QD=18.30;ReadPosRankSum=-1.232;SOR=1.300 GT:AD:DP:GQ:PL 0/1:33,30:63:99:1160,0,1477 +20 10032972 . C CAT 1152.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.354;DP=65;ExcessHet=3.0103;FS=5.062;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=-1.017;QD=18.30;ReadPosRankSum=-1.232;SOR=1.300 GT:AD:DP:GQ:PL 0/1:33,30:63:99:1160,0,1295 20 10034306 . T C 803.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.661;DP=76;ExcessHet=3.0103;FS=0.890;MLEAC=1;MLEAF=0.500;MQ=59.45;MQRankSum=1.150;QD=10.71;ReadPosRankSum=0.539;SOR=0.685 GT:AD:DP:GQ:PL 0/1:46,29:75:99:811,0,1593 -20 10036930 . CGATAGCCCTAGCCCTAGATA C 1066.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.200;DP=93;ExcessHet=3.0103;FS=11.152;MLEAC=1;MLEAF=0.500;MQ=54.36;MQRankSum=-4.048;QD=15.69;ReadPosRankSum=0.460;SOR=0.269 GT:AD:DP:GQ:PL 0/1:39,29:68:99:1074,0,5569 +20 10036930 . CGATAGCCCTAGCCCTAGATA C 1066.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.200;DP=93;ExcessHet=3.0103;FS=11.152;MLEAC=1;MLEAF=0.500;MQ=54.36;MQRankSum=-4.048;QD=15.69;ReadPosRankSum=0.460;SOR=0.269 GT:AD:DP:GQ:PL 0/1:39,29:68:99:1074,0,1504 20 10037037 . C T 1457.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.504;DP=81;ExcessHet=3.0103;FS=1.943;MLEAC=1;MLEAF=0.500;MQ=60.17;MQRankSum=-1.193;QD=18.00;ReadPosRankSum=-1.609;SOR=0.495 GT:AD:DP:GQ:PL 0/1:39,42:81:99:1465,0,1124 20 10037110 . T TGATA 2804.06 . AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.98;QD=34.66;SOR=1.022 GT:AD:DP:GQ:PL 1/1:0,61:61:99:2818,189,0 20 10037144 . T TGATAGATA 1847.06 . AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.73;QD=29.40;SOR=1.061 GT:AD:DP:GQ:PL 1/1:0,36:36:99:1861,127,0 @@ -162,7 +162,7 @@ 20 10042319 . C T 2673.03 . AC=2;AF=1.00;AN=2;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.01;QD=21.53;SOR=1.033 GT:AD:DP:GQ:PL 1/1:0,66:66:99:2687,199,0 20 10042761 . A G 3568.03 . AC=2;AF=1.00;AN=2;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.87;SOR=1.389 GT:AD:DP:GQ:PL 1/1:0,91:91:99:3582,272,0 20 10042829 . A G 3070.03 . AC=2;AF=1.00;AN=2;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.76;QD=31.04;SOR=0.855 GT:AD:DP:GQ:PL 1/1:0,78:78:99:3084,235,0 -20 10043002 . A T 1308.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.986;DP=86;ExcessHet=3.0103;FS=2.877;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=15.22;ReadPosRankSum=-0.035;SOR=0.434 GT:AD:DP:GQ:PL 0/1:48,38:86:99:1316,0,1659 +20 10043002 . A T 1308.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.986;DP=86;ExcessHet=3.0103;FS=2.877;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=15.22;ReadPosRankSum=-0.035;SOR=0.434 GT:AD:DP:GQ:PL 0/1:48,38:86:99:1316,0,1658 20 10044849 . A G 2106.03 . AC=2;AF=1.00;AN=2;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.61;QD=27.86;SOR=1.316 GT:AD:DP:GQ:PL 1/1:0,59:59:99:2120,177,0 20 10045078 . G T 3286.03 . AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.73;QD=34.17;SOR=0.876 GT:AD:DP:GQ:PL 1/1:0,81:81:99:3300,244,0 20 10045642 . G C 3153.03 . AC=2;AF=1.00;AN=2;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.49;QD=28.60;SOR=0.846 GT:AD:DP:GQ:PL 1/1:0,82:82:99:3167,246,0 @@ -221,23 +221,23 @@ 20 10088747 . A G 1132.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.877;DP=54;ExcessHet=3.0103;FS=7.653;MLEAC=1;MLEAF=0.500;MQ=51.89;MQRankSum=-4.907;QD=20.97;ReadPosRankSum=0.009;SOR=1.092 GT:AD:DP:GQ:PL 0/1:25,29:54:99:1140,0,995 20 10088799 . G A 1039.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=5.503;DP=53;ExcessHet=3.0103;FS=10.098;MLEAC=1;MLEAF=0.500;MQ=53.21;MQRankSum=-2.498;QD=19.62;ReadPosRankSum=1.075;SOR=1.003 GT:AD:DP:GQ:PL 0/1:22,31:53:99:1047,0,617 20 10088895 . C T 553.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.462;DP=41;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.26;MQRankSum=0.577;QD=13.50;ReadPosRankSum=1.301;SOR=0.653 GT:AD:DP:GQ:PL 0/1:23,18:41:99:561,0,673 -20 10088968 . C CAAA 1205.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.552;DP=62;ExcessHet=3.0103;FS=1.078;MLEAC=1;MLEAF=0.500;MQ=53.55;MQRankSum=-4.750;QD=22.75;ReadPosRankSum=2.416;SOR=1.012 GT:AD:DP:GQ:PL 0/1:30,23:53:99:1213,0,1367 -20 10088980 . T C 1268.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.585;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.93;MQRankSum=-5.232;QD=18.66;ReadPosRankSum=1.288;SOR=0.709 GT:AD:DP:GQ:PL 0/1:37,31:68:99:1276,0,1627 -20 10088985 . T C 1199.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.192;DP=74;ExcessHet=3.0103;FS=0.890;MLEAC=1;MLEAF=0.500;MQ=50.91;MQRankSum=-5.248;QD=16.21;ReadPosRankSum=1.228;SOR=0.742 GT:AD:DP:GQ:PL 0/1:42,32:74:99:1207,0,1729 +20 10088968 . C CAAA 1205.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.552;DP=62;ExcessHet=3.0103;FS=1.078;MLEAC=1;MLEAF=0.500;MQ=53.55;MQRankSum=-4.750;QD=22.75;ReadPosRankSum=2.416;SOR=1.012 GT:AD:DP:GQ:PL 0/1:30,23:53:99:1213,0,1236 +20 10088980 . T C 1268.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.585;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.93;MQRankSum=-5.232;QD=18.66;ReadPosRankSum=1.288;SOR=0.709 GT:AD:DP:GQ:PL 0/1:37,31:68:99:1276,0,1497 +20 10088985 . T C 1199.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.192;DP=74;ExcessHet=3.0103;FS=0.890;MLEAC=1;MLEAF=0.500;MQ=50.91;MQRankSum=-5.248;QD=16.21;ReadPosRankSum=1.228;SOR=0.742 GT:AD:DP:GQ:PL 0/1:42,32:74:99:1207,0,1599 20 10089441 . A G 1200.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-4.885;DP=76;ExcessHet=3.0103;FS=6.071;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=-0.948;QD=15.80;ReadPosRankSum=-0.156;SOR=1.363 GT:AD:DP:GQ:PL 0/1:37,39:76:99:1208,0,1313 20 10089525 . C T 1569.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=5.859;DP=81;ExcessHet=3.0103;FS=4.260;MLEAC=1;MLEAF=0.500;MQ=59.48;MQRankSum=1.531;QD=19.38;ReadPosRankSum=0.862;SOR=0.617 GT:AD:DP:GQ:PL 0/1:38,43:81:99:1577,0,1088 20 10090289 . CA C 414.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.316;DP=79;ExcessHet=3.0103;FS=1.377;MLEAC=1;MLEAF=0.500;MQ=59.97;MQRankSum=1.531;QD=10.91;ReadPosRankSum=0.535;SOR=1.127 GT:AD:DP:GQ:PL 0/1:14,24:38:99:422,0,230 20 10090764 . A G 861.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.659;DP=63;ExcessHet=3.0103;FS=4.975;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=13.68;ReadPosRankSum=1.207;SOR=0.310 GT:AD:DP:GQ:PL 0/1:34,29:63:99:869,0,1207 20 10090970 . T C 1278.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.484;DP=69;ExcessHet=3.0103;FS=0.927;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=1.509;QD=18.53;ReadPosRankSum=-0.072;SOR=0.518 GT:AD:DP:GQ:PL 0/1:33,36:69:99:1286,0,1092 20 10091214 . C T 1270.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.361;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=-0.916;QD=18.15;ReadPosRankSum=-0.035;SOR=0.625 GT:AD:DP:GQ:PL 0/1:33,37:70:99:1278,0,1110 -20 10092415 . A G 1656.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-6.731;DP=101;ExcessHet=3.0103;FS=0.741;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=16.40;ReadPosRankSum=0.082;SOR=0.665 GT:AD:DP:GQ:PL 0/1:52,49:101:99:1664,0,1902 +20 10092415 . A G 1656.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-6.731;DP=101;ExcessHet=3.0103;FS=0.741;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=16.40;ReadPosRankSum=0.082;SOR=0.665 GT:AD:DP:GQ:PL 0/1:52,49:101:99:1664,0,1901 20 10092927 . G T 127.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.507;DP=73;ExcessHet=3.0103;FS=60.191;MLEAC=1;MLEAF=0.500;MQ=59.37;MQRankSum=-3.009;QD=1.77;ReadPosRankSum=-0.220;SOR=5.279 GT:AD:DP:GQ:PL 0/1:59,13:72:99:135,0,1864 20 10093568 . GT G 356.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.131;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQRankSum=1.078;QD=8.29;ReadPosRankSum=0.655;SOR=0.693 GT:AD:DP:GQ:PL 0/1:22,21:43:99:364,0,386 20 10093923 . T A 1096.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.667;DP=67;ExcessHet=3.0103;FS=0.924;MLEAC=1;MLEAF=0.500;MQ=59.19;MQRankSum=0.358;QD=16.37;ReadPosRankSum=-1.583;SOR=0.772 GT:AD:DP:GQ:PL 0/1:35,32:67:99:1104,0,1257 20 10094251 . T A 1291.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.251;DP=62;ExcessHet=3.0103;FS=11.483;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=20.83;ReadPosRankSum=1.806;SOR=1.211 GT:AD:DP:GQ:PL 0/1:26,36:62:99:1299,0,781 20 10094582 . A G 944.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.388;DP=69;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.39;MQRankSum=1.270;QD=13.69;ReadPosRankSum=-0.018;SOR=0.772 GT:AD:DP:GQ:PL 0/1:39,30:69:99:952,0,1350 20 10094774 . C T 1057.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.784;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.69;MQRankSum=0.962;QD=14.10;ReadPosRankSum=0.197;SOR=0.690 GT:AD:DP:GQ:PL 0/1:40,35:75:99:1065,0,1282 -20 10095432 . GTGATGATGA G 869.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.265;DP=77;ExcessHet=3.0103;FS=1.102;MLEAC=1;MLEAF=0.500;MQ=54.39;MQRankSum=-4.431;QD=17.39;ReadPosRankSum=0.396;SOR=0.460 GT:AD:DP:GQ:PL 0/1:27,23:50:99:877,0,2108 +20 10095432 . GTGATGATGA G 870.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.265;DP=77;ExcessHet=3.0103;FS=1.102;MLEAC=1;MLEAF=0.500;MQ=54.39;MQRankSum=-4.431;QD=17.41;ReadPosRankSum=0.396;SOR=0.460 GT:AD:DP:GQ:PL 0/1:27,23:50:99:878,0,998 20 10095741 . A G 1096.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.534;DP=71;ExcessHet=3.0103;FS=4.721;MLEAC=1;MLEAF=0.500;MQ=57.35;MQRankSum=-2.313;QD=15.67;ReadPosRankSum=-0.500;SOR=0.515 GT:AD:DP:GQ:PL 0/1:36,34:70:99:1104,0,1233 20 10096293 . C T 1376.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.664;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.57;MQRankSum=1.397;QD=18.35;ReadPosRankSum=-1.135;SOR=0.638 GT:AD:DP:GQ:PL 0/1:37,38:75:99:1384,0,1258 20 10096596 . C T 1583.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.728;DP=87;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.77;MQRankSum=0.612;QD=18.20;ReadPosRankSum=-0.170;SOR=0.640 GT:AD:DP:GQ:PL 0/1:40,47:87:99:1591,0,1273 @@ -247,7 +247,7 @@ 20 10096933 . G C 1532.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.914;DP=85;ExcessHet=3.0103;FS=23.320;MLEAC=1;MLEAF=0.500;MQ=59.29;MQRankSum=-1.802;QD=18.03;ReadPosRankSum=0.334;SOR=1.534 GT:AD:DP:GQ:PL 0/1:44,41:85:99:1540,0,1770 20 10096958 . G A 1787.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.839;DP=92;ExcessHet=3.0103;FS=16.778;MLEAC=1;MLEAF=0.500;MQ=59.34;MQRankSum=-1.701;QD=19.43;ReadPosRankSum=-1.833;SOR=1.387 GT:AD:DP:GQ:PL 0/1:45,47:92:99:1795,0,1629 20 10097075 . T G 1466.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.533;DP=92;ExcessHet=3.0103;FS=6.613;MLEAC=1;MLEAF=0.500;MQ=58.57;MQRankSum=-1.389;QD=15.94;ReadPosRankSum=0.082;SOR=0.628 GT:AD:DP:GQ:PL 0/1:44,48:92:99:1474,0,1482 -20 10097101 . C CTTT 1121.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.894;DP=76;ExcessHet=3.0103;FS=7.156;MLEAC=1;MLEAF=0.500;MQ=57.62;MQRankSum=-1.750;QD=16.99;ReadPosRankSum=2.739;SOR=0.501 GT:AD:DP:GQ:PL 0/1:34,32:66:99:1129,0,1306 +20 10097101 . C CTTT 1121.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.894;DP=76;ExcessHet=3.0103;FS=7.156;MLEAC=1;MLEAF=0.500;MQ=57.62;MQRankSum=-1.750;QD=16.99;ReadPosRankSum=2.739;SOR=0.501 GT:AD:DP:GQ:PL 0/1:34,32:66:99:1129,0,1259 20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C 1084.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.820;DP=89;ExcessHet=3.0103;FS=1.851;MLEAC=1;MLEAF=0.500;MQ=54.27;MQRankSum=-6.464;QD=12.19;ReadPosRankSum=-3.097;SOR=0.948 GT:AD:DP:GQ:PL 0/1:57,32:89:99:1092,0,2241 20 10097437 . TTTTC *,T 930.01 . AC=1,1;AF=0.500,0.500;AN=2;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=53.48;QD=16.91;SOR=1.877 GT:AD:DP:GQ:PL 1/2:0,32,23:55:99:2127,940,1799,1196,0,1125 20 10097626 . C A 647.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.085;DP=48;ExcessHet=3.0103;FS=2.701;MLEAC=1;MLEAF=0.500;MQ=58.24;MQRankSum=-1.331;QD=13.49;ReadPosRankSum=1.015;SOR=0.324 GT:AD:DP:GQ:PL 0/1:28,20:48:99:655,0,957 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.vcf index 921ebe5c821..2ee19b46fb8 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/expected.testVCFMode.gatk4.vcf @@ -83,8 +83,8 @@ 20 10008742 . G T 736.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.893;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=37.22;MQRankSum=-1.502;QD=15.03;ReadPosRankSum=0.190;SOR=0.741 GT:AD:DP:GQ:PL 0/1:23,26:49:99:744,0,580 20 10008758 . C CA 707.53 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.130;DP=44;ExcessHet=3.0103;FS=2.160;MLEAC=1;MLEAF=0.500;MQ=35.24;MQRankSum=-1.168;QD=20.22;ReadPosRankSum=-0.052;SOR=0.249 GT:AD:DP:GQ:PL 1/1:4,31:35:10:721,10,0 20 10008921 . C CA 283.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.610;DP=49;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=56.34;MQRankSum=-1.906;QD=8.34;ReadPosRankSum=0.173;SOR=0.512 GT:AD:DP:GQ:PL 0/1:18,16:34:99:291,0,366 -20 10008948 . TA T 2081.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.994;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.63;MQRankSum=2.047;QD=27.08;ReadPosRankSum=0.884;SOR=0.818 GT:AD:DP:GQ:PL 1/1:1,50:51:99:2095,107,0 -20 10008952 . CACACACACACA C,CCACACACACA 1687.10 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.963;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=51.10;MQRankSum=1.976;QD=25.42;ReadPosRankSum=0.934;SOR=1.112 GT:AD:DP:GQ:PL 1/2:1,17,18:36:99:1704,525,844,582,0,531 +20 10008948 . TA T 2092.03 . AC=2;AF=1.00;AN=2;BaseQRankSum=0.994;DP=52;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.63;MQRankSum=2.047;QD=27.08;ReadPosRankSum=0.884;SOR=0.818 GT:AD:DP:GQ:PL 1/1:1,50:51:99:2106,117,0 +20 10008952 . CACACACACACA C,CCACACACACA 1701.10 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=0.963;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=51.10;MQRankSum=1.976;QD=25.42;ReadPosRankSum=0.934;SOR=1.112 GT:AD:DP:GQ:PL 1/2:1,17,18:36:99:1718,539,802,596,0,534 20 10009227 . A G 1390.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.220;DP=62;ExcessHet=3.0103;FS=9.110;MLEAC=1;MLEAF=0.500;MQ=57.16;MQRankSum=1.428;QD=22.43;ReadPosRankSum=-1.159;SOR=0.281 GT:AD:DP:GQ:PL 0/1:23,39:62:99:1398,0,740 20 10009246 . A G 3017.03 . AC=2;AF=1.00;AN=2;DP=77;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.09;QD=27.65;SOR=0.887 GT:AD:DP:GQ:PL 1/1:0,77:77:99:3031,231,0 20 10009400 . T A 3013.03 . AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=29.48;SOR=0.804 GT:AD:DP:GQ:PL 1/1:0,74:74:99:3027,223,0 @@ -134,9 +134,9 @@ 20 10024300 . C CTT 104.67 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.362;DP=50;ExcessHet=3.0103;FS=3.090;MLEAC=1;MLEAF=0.500;MQ=51.90;MQRankSum=-0.084;QD=6.16;ReadPosRankSum=-0.431;SOR=1.773 GT:AD:DP:GQ:PL 0/1:9,8:17:99:103,0,137 20 10026357 . T C 1187.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.700;DP=63;ExcessHet=3.0103;FS=8.911;MLEAC=1;MLEAF=0.500;MQ=58.43;MQRankSum=-0.148;QD=18.85;ReadPosRankSum=-0.076;SOR=0.722 GT:AD:DP:GQ:PL 0/1:28,35:63:99:1195,0,932 20 10026794 . C T 1105.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.828;DP=52;ExcessHet=3.0103;FS=2.399;MLEAC=1;MLEAF=0.500;MQ=59.56;MQRankSum=-0.719;QD=21.26;ReadPosRankSum=-0.533;SOR=0.428 GT:AD:DP:GQ:PL 0/1:19,33:52:99:1113,0,529 -20 10027234 . A ATTAG 1350.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.406;DP=72;ExcessHet=3.0103;FS=3.248;MLEAC=1;MLEAF=0.500;MQ=57.33;MQRankSum=-0.845;QD=19.57;ReadPosRankSum=-0.979;SOR=0.926 GT:AD:DP:GQ:PL 0/1:34,35:69:99:1358,0,1964 -20 10027868 . A G 1760.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-5.793;DP=89;ExcessHet=3.0103;FS=6.868;MLEAC=1;MLEAF=0.500;MQ=59.48;MQRankSum=0.032;QD=19.78;ReadPosRankSum=1.872;SOR=0.881 GT:AD:DP:GQ:PL 0/1:44,45:89:99:1768,0,3201 -20 10027872 . A G 1745.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-5.491;DP=85;ExcessHet=3.0103;FS=8.870;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=0.101;QD=20.54;ReadPosRankSum=1.053;SOR=0.826 GT:AD:DP:GQ:PL 0/1:40,45:85:99:1753,0,3136 +20 10027234 . A ATTAG 1350.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.406;DP=72;ExcessHet=3.0103;FS=3.248;MLEAC=1;MLEAF=0.500;MQ=57.33;MQRankSum=-0.845;QD=19.57;ReadPosRankSum=-0.979;SOR=0.926 GT:AD:DP:GQ:PL 0/1:34,35:69:99:1358,0,1320 +20 10027868 . A G 1760.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-5.793;DP=89;ExcessHet=3.0103;FS=6.868;MLEAC=1;MLEAF=0.500;MQ=59.48;MQRankSum=0.032;QD=19.78;ReadPosRankSum=1.872;SOR=0.881 GT:AD:DP:GQ:PL 0/1:44,45:89:99:1768,0,1671 +20 10027872 . A G 1745.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-5.491;DP=85;ExcessHet=3.0103;FS=8.870;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=0.101;QD=20.54;ReadPosRankSum=1.053;SOR=0.826 GT:AD:DP:GQ:PL 0/1:40,45:85:99:1753,0,1606 20 10028867 . A ATG 1136.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.874;DP=92;ExcessHet=3.0103;FS=4.652;MLEAC=1;MLEAF=0.500;MQ=60.69;MQRankSum=2.711;QD=16.01;ReadPosRankSum=0.364;SOR=0.336 GT:AD:DP:GQ:PL 0/1:32,39:71:99:1144,0,916 20 10030188 . T A 1393.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.711;DP=81;ExcessHet=3.0103;FS=9.186;MLEAC=1;MLEAF=0.500;MQ=59.72;MQRankSum=-1.013;QD=17.20;ReadPosRankSum=-0.553;SOR=1.105 GT:AD:DP:GQ:PL 0/1:42,39:81:99:1401,0,1524 20 10031254 . A AT 1493.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.091;DP=86;ExcessHet=3.0103;FS=9.250;MLEAC=1;MLEAF=0.500;MQ=59.91;MQRankSum=0.017;QD=17.57;ReadPosRankSum=0.495;SOR=0.211 GT:AD:DP:GQ:PL 0/1:38,47:85:99:1501,0,1159 @@ -146,9 +146,9 @@ 20 10032094 . G A 1241.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=5.488;DP=83;ExcessHet=3.0103;FS=6.039;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=14.96;ReadPosRankSum=-0.579;SOR=0.260 GT:AD:DP:GQ:PL 0/1:47,36:83:99:1249,0,1497 20 10032413 . T G 890.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-6.142;DP=66;ExcessHet=3.0103;FS=10.444;MLEAC=1;MLEAF=0.500;MQ=59.43;MQRankSum=-0.065;QD=13.49;ReadPosRankSum=-1.003;SOR=1.293 GT:AD:DP:GQ:PL 0/1:35,31:66:99:898,0,1277 20 10032882 . A T 1223.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.697;DP=75;ExcessHet=3.0103;FS=4.673;MLEAC=1;MLEAF=0.500;MQ=59.69;MQRankSum=-1.014;QD=16.31;ReadPosRankSum=0.626;SOR=0.338 GT:AD:DP:GQ:PL 0/1:39,36:75:99:1231,0,1406 -20 10032972 . C CAT 1152.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.354;DP=65;ExcessHet=3.0103;FS=5.062;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=-1.017;QD=18.30;ReadPosRankSum=-1.232;SOR=1.300 GT:AD:DP:GQ:PL 0/1:33,30:63:99:1160,0,1477 +20 10032972 . C CAT 1152.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.354;DP=65;ExcessHet=3.0103;FS=5.062;MLEAC=1;MLEAF=0.500;MQ=59.65;MQRankSum=-1.017;QD=18.30;ReadPosRankSum=-1.232;SOR=1.300 GT:AD:DP:GQ:PL 0/1:33,30:63:99:1160,0,1295 20 10034306 . T C 803.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.661;DP=76;ExcessHet=3.0103;FS=0.890;MLEAC=1;MLEAF=0.500;MQ=59.45;MQRankSum=1.150;QD=10.71;ReadPosRankSum=0.539;SOR=0.685 GT:AD:DP:GQ:PL 0/1:46,29:75:99:811,0,1593 -20 10036930 . CGATAGCCCTAGCCCTAGATA C 1066.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.200;DP=93;ExcessHet=3.0103;FS=11.152;MLEAC=1;MLEAF=0.500;MQ=54.36;MQRankSum=-4.048;QD=15.69;ReadPosRankSum=0.460;SOR=0.269 GT:AD:DP:GQ:PL 0/1:39,29:68:99:1074,0,5569 +20 10036930 . CGATAGCCCTAGCCCTAGATA C 1066.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.200;DP=93;ExcessHet=3.0103;FS=11.152;MLEAC=1;MLEAF=0.500;MQ=54.36;MQRankSum=-4.048;QD=15.69;ReadPosRankSum=0.460;SOR=0.269 GT:AD:DP:GQ:PL 0/1:39,29:68:99:1074,0,1504 20 10037037 . C T 1457.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.504;DP=81;ExcessHet=3.0103;FS=1.943;MLEAC=1;MLEAF=0.500;MQ=60.17;MQRankSum=-1.193;QD=18.00;ReadPosRankSum=-1.609;SOR=0.495 GT:AD:DP:GQ:PL 0/1:39,42:81:99:1465,0,1124 20 10037110 . T TGATA 2804.06 . AC=2;AF=1.00;AN=2;DP=74;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=56.98;QD=34.66;SOR=1.022 GT:AD:DP:GQ:PL 1/1:0,61:61:99:2818,189,0 20 10037144 . T TGATAGATA 1847.06 . AC=2;AF=1.00;AN=2;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=51.73;QD=29.40;SOR=1.061 GT:AD:DP:GQ:PL 1/1:0,36:36:99:1861,127,0 @@ -162,7 +162,7 @@ 20 10042319 . C T 2673.03 . AC=2;AF=1.00;AN=2;DP=66;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.01;QD=21.53;SOR=1.033 GT:AD:DP:GQ:PL 1/1:0,66:66:99:2687,199,0 20 10042761 . A G 3568.03 . AC=2;AF=1.00;AN=2;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=34.87;SOR=1.389 GT:AD:DP:GQ:PL 1/1:0,91:91:99:3582,272,0 20 10042829 . A G 3070.03 . AC=2;AF=1.00;AN=2;DP=78;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.76;QD=31.04;SOR=0.855 GT:AD:DP:GQ:PL 1/1:0,78:78:99:3084,235,0 -20 10043002 . A T 1308.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.986;DP=86;ExcessHet=3.0103;FS=2.877;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=15.22;ReadPosRankSum=-0.035;SOR=0.434 GT:AD:DP:GQ:PL 0/1:48,38:86:99:1316,0,1659 +20 10043002 . A T 1308.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=3.986;DP=86;ExcessHet=3.0103;FS=2.877;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=15.22;ReadPosRankSum=-0.035;SOR=0.434 GT:AD:DP:GQ:PL 0/1:48,38:86:99:1316,0,1658 20 10044849 . A G 2106.03 . AC=2;AF=1.00;AN=2;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.61;QD=27.86;SOR=1.316 GT:AD:DP:GQ:PL 1/1:0,59:59:99:2120,177,0 20 10045078 . G T 3286.03 . AC=2;AF=1.00;AN=2;DP=81;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=58.73;QD=34.17;SOR=0.876 GT:AD:DP:GQ:PL 1/1:0,81:81:99:3300,244,0 20 10045642 . G C 3153.03 . AC=2;AF=1.00;AN=2;DP=82;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=59.49;QD=28.60;SOR=0.846 GT:AD:DP:GQ:PL 1/1:0,82:82:99:3167,246,0 @@ -221,23 +221,23 @@ 20 10088747 . A G 1132.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-3.877;DP=54;ExcessHet=3.0103;FS=7.653;MLEAC=1;MLEAF=0.500;MQ=51.89;MQRankSum=-4.907;QD=20.97;ReadPosRankSum=0.009;SOR=1.092 GT:AD:DP:GQ:PL 0/1:25,29:54:99:1140,0,995 20 10088799 . G A 1039.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=5.503;DP=53;ExcessHet=3.0103;FS=10.098;MLEAC=1;MLEAF=0.500;MQ=53.21;MQRankSum=-2.498;QD=19.62;ReadPosRankSum=1.075;SOR=1.003 GT:AD:DP:GQ:PL 0/1:22,31:53:99:1047,0,617 20 10088895 . C T 553.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.462;DP=41;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=57.26;MQRankSum=0.577;QD=13.50;ReadPosRankSum=1.301;SOR=0.653 GT:AD:DP:GQ:PL 0/1:23,18:41:99:561,0,673 -20 10088968 . C CAAA 1205.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.552;DP=62;ExcessHet=3.0103;FS=1.078;MLEAC=1;MLEAF=0.500;MQ=53.55;MQRankSum=-4.750;QD=22.75;ReadPosRankSum=2.416;SOR=1.012 GT:AD:DP:GQ:PL 0/1:30,23:53:99:1213,0,1367 -20 10088980 . T C 1268.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.585;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.93;MQRankSum=-5.232;QD=18.66;ReadPosRankSum=1.288;SOR=0.709 GT:AD:DP:GQ:PL 0/1:37,31:68:99:1276,0,1627 -20 10088985 . T C 1199.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.192;DP=74;ExcessHet=3.0103;FS=0.890;MLEAC=1;MLEAF=0.500;MQ=50.91;MQRankSum=-5.248;QD=16.21;ReadPosRankSum=1.228;SOR=0.742 GT:AD:DP:GQ:PL 0/1:42,32:74:99:1207,0,1729 +20 10088968 . C CAAA 1205.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.552;DP=62;ExcessHet=3.0103;FS=1.078;MLEAC=1;MLEAF=0.500;MQ=53.55;MQRankSum=-4.750;QD=22.75;ReadPosRankSum=2.416;SOR=1.012 GT:AD:DP:GQ:PL 0/1:30,23:53:99:1213,0,1236 +20 10088980 . T C 1268.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.585;DP=68;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=50.93;MQRankSum=-5.232;QD=18.66;ReadPosRankSum=1.288;SOR=0.709 GT:AD:DP:GQ:PL 0/1:37,31:68:99:1276,0,1497 +20 10088985 . T C 1199.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.192;DP=74;ExcessHet=3.0103;FS=0.890;MLEAC=1;MLEAF=0.500;MQ=50.91;MQRankSum=-5.248;QD=16.21;ReadPosRankSum=1.228;SOR=0.742 GT:AD:DP:GQ:PL 0/1:42,32:74:99:1207,0,1599 20 10089441 . A G 1200.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-4.885;DP=76;ExcessHet=3.0103;FS=6.071;MLEAC=1;MLEAF=0.500;MQ=59.70;MQRankSum=-0.948;QD=15.80;ReadPosRankSum=-0.156;SOR=1.363 GT:AD:DP:GQ:PL 0/1:37,39:76:99:1208,0,1313 20 10089525 . C T 1569.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=5.859;DP=81;ExcessHet=3.0103;FS=4.260;MLEAC=1;MLEAF=0.500;MQ=59.48;MQRankSum=1.531;QD=19.38;ReadPosRankSum=0.862;SOR=0.617 GT:AD:DP:GQ:PL 0/1:38,43:81:99:1577,0,1088 20 10090289 . CA C 414.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.316;DP=79;ExcessHet=3.0103;FS=1.377;MLEAC=1;MLEAF=0.500;MQ=59.97;MQRankSum=1.531;QD=10.91;ReadPosRankSum=0.535;SOR=1.127 GT:AD:DP:GQ:PL 0/1:14,24:38:99:422,0,230 20 10090764 . A G 861.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.659;DP=63;ExcessHet=3.0103;FS=4.975;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=13.68;ReadPosRankSum=1.207;SOR=0.310 GT:AD:DP:GQ:PL 0/1:34,29:63:99:869,0,1207 20 10090970 . T C 1278.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.484;DP=69;ExcessHet=3.0103;FS=0.927;MLEAC=1;MLEAF=0.500;MQ=59.46;MQRankSum=1.509;QD=18.53;ReadPosRankSum=-0.072;SOR=0.518 GT:AD:DP:GQ:PL 0/1:33,36:69:99:1286,0,1092 20 10091214 . C T 1270.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.361;DP=70;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.73;MQRankSum=-0.916;QD=18.15;ReadPosRankSum=-0.035;SOR=0.625 GT:AD:DP:GQ:PL 0/1:33,37:70:99:1278,0,1110 -20 10092415 . A G 1656.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-6.731;DP=101;ExcessHet=3.0103;FS=0.741;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=16.40;ReadPosRankSum=0.082;SOR=0.665 GT:AD:DP:GQ:PL 0/1:52,49:101:99:1664,0,1902 +20 10092415 . A G 1656.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-6.731;DP=101;ExcessHet=3.0103;FS=0.741;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=16.40;ReadPosRankSum=0.082;SOR=0.665 GT:AD:DP:GQ:PL 0/1:52,49:101:99:1664,0,1901 20 10092927 . G T 127.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.507;DP=73;ExcessHet=3.0103;FS=60.191;MLEAC=1;MLEAF=0.500;MQ=59.37;MQRankSum=-3.009;QD=1.77;ReadPosRankSum=-0.220;SOR=5.279 GT:AD:DP:GQ:PL 0/1:59,13:72:99:135,0,1864 20 10093568 . GT G 356.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.131;DP=59;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.74;MQRankSum=1.078;QD=8.29;ReadPosRankSum=0.655;SOR=0.693 GT:AD:DP:GQ:PL 0/1:22,21:43:99:364,0,386 20 10093923 . T A 1096.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.667;DP=67;ExcessHet=3.0103;FS=0.924;MLEAC=1;MLEAF=0.500;MQ=59.19;MQRankSum=0.358;QD=16.37;ReadPosRankSum=-1.583;SOR=0.772 GT:AD:DP:GQ:PL 0/1:35,32:67:99:1104,0,1257 20 10094251 . T A 1291.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.251;DP=62;ExcessHet=3.0103;FS=11.483;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=20.83;ReadPosRankSum=1.806;SOR=1.211 GT:AD:DP:GQ:PL 0/1:26,36:62:99:1299,0,781 20 10094582 . A G 944.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.388;DP=69;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.39;MQRankSum=1.270;QD=13.69;ReadPosRankSum=-0.018;SOR=0.772 GT:AD:DP:GQ:PL 0/1:39,30:69:99:952,0,1350 20 10094774 . C T 1057.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.784;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=59.69;MQRankSum=0.962;QD=14.10;ReadPosRankSum=0.197;SOR=0.690 GT:AD:DP:GQ:PL 0/1:40,35:75:99:1065,0,1282 -20 10095432 . GTGATGATGA G 869.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.265;DP=77;ExcessHet=3.0103;FS=1.102;MLEAC=1;MLEAF=0.500;MQ=54.39;MQRankSum=-4.431;QD=17.39;ReadPosRankSum=0.396;SOR=0.460 GT:AD:DP:GQ:PL 0/1:27,23:50:99:877,0,2108 +20 10095432 . GTGATGATGA G 870.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.265;DP=77;ExcessHet=3.0103;FS=1.102;MLEAC=1;MLEAF=0.500;MQ=54.39;MQRankSum=-4.431;QD=17.41;ReadPosRankSum=0.396;SOR=0.460 GT:AD:DP:GQ:PL 0/1:27,23:50:99:878,0,998 20 10095741 . A G 1096.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.534;DP=71;ExcessHet=3.0103;FS=4.721;MLEAC=1;MLEAF=0.500;MQ=57.35;MQRankSum=-2.313;QD=15.67;ReadPosRankSum=-0.500;SOR=0.515 GT:AD:DP:GQ:PL 0/1:36,34:70:99:1104,0,1233 20 10096293 . C T 1376.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=4.664;DP=75;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.57;MQRankSum=1.397;QD=18.35;ReadPosRankSum=-1.135;SOR=0.638 GT:AD:DP:GQ:PL 0/1:37,38:75:99:1384,0,1258 20 10096596 . C T 1583.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.728;DP=87;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=58.77;MQRankSum=0.612;QD=18.20;ReadPosRankSum=-0.170;SOR=0.640 GT:AD:DP:GQ:PL 0/1:40,47:87:99:1591,0,1273 @@ -247,7 +247,7 @@ 20 10096933 . G C 1532.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.914;DP=85;ExcessHet=3.0103;FS=23.320;MLEAC=1;MLEAF=0.500;MQ=59.29;MQRankSum=-1.802;QD=18.03;ReadPosRankSum=0.334;SOR=1.534 GT:AD:DP:GQ:PL 0/1:44,41:85:99:1540,0,1770 20 10096958 . G A 1787.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=2.839;DP=92;ExcessHet=3.0103;FS=16.778;MLEAC=1;MLEAF=0.500;MQ=59.34;MQRankSum=-1.701;QD=19.43;ReadPosRankSum=-1.833;SOR=1.387 GT:AD:DP:GQ:PL 0/1:45,47:92:99:1795,0,1629 20 10097075 . T G 1466.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-2.533;DP=92;ExcessHet=3.0103;FS=6.613;MLEAC=1;MLEAF=0.500;MQ=58.57;MQRankSum=-1.389;QD=15.94;ReadPosRankSum=0.082;SOR=0.628 GT:AD:DP:GQ:PL 0/1:44,48:92:99:1474,0,1482 -20 10097101 . C CTTT 1121.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.894;DP=76;ExcessHet=3.0103;FS=7.156;MLEAC=1;MLEAF=0.500;MQ=57.62;MQRankSum=-1.750;QD=16.99;ReadPosRankSum=2.739;SOR=0.501 GT:AD:DP:GQ:PL 0/1:34,32:66:99:1129,0,1306 +20 10097101 . C CTTT 1121.64 . AC=1;AF=0.500;AN=2;BaseQRankSum=-0.894;DP=76;ExcessHet=3.0103;FS=7.156;MLEAC=1;MLEAF=0.500;MQ=57.62;MQRankSum=-1.750;QD=16.99;ReadPosRankSum=2.739;SOR=0.501 GT:AD:DP:GQ:PL 0/1:34,32:66:99:1129,0,1259 20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C 1084.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.820;DP=89;ExcessHet=3.0103;FS=1.851;MLEAC=1;MLEAF=0.500;MQ=54.27;MQRankSum=-6.464;QD=12.19;ReadPosRankSum=-3.097;SOR=0.948 GT:AD:DP:GQ:PL 0/1:57,32:89:99:1092,0,2241 20 10097437 . TTTTC *,T 930.01 . AC=1,1;AF=0.500,0.500;AN=2;DP=76;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=53.48;QD=16.91;SOR=1.877 GT:AD:DP:GQ:PL 1/2:0,32,23:55:99:2127,940,1799,1196,0,1125 20 10097626 . C A 647.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=1.085;DP=48;ExcessHet=3.0103;FS=2.701;MLEAC=1;MLEAF=0.500;MQ=58.24;MQRankSum=-1.331;QD=13.49;ReadPosRankSum=1.015;SOR=0.324 GT:AD:DP:GQ:PL 0/1:28,20:48:99:655,0,957 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/IntervalTest.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/IntervalTest.vcf index a577c4d4a12..ed4e281b587 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/IntervalTest.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/IntervalTest.vcf @@ -8,20 +8,113 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine.CombineGVCFs= +##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) +##INFO= +##INFO= +##INFO= ##INFO= ##INFO= ##INFO= ##INFO= +##INFO= +##INFO= ##INFO= +##INFO= ##INFO= ##INFO= ##INFO= +##INFO= ##INFO= -##contig= -##contig= -##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +##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:///Users/ebanks/Sting_unstable/../references/hs37d5.fasta +##source=CombineGVCFs ##source=SelectVariants #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA1 NA2 20 69491 . G . . END=69497 GT:DP:GQ:MIN_DP:MIN_GQ:PL ./.:94:99:82:99:0,120,1800 ./. diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/IntervalTest.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/IntervalTest.vcf.idx index 6d66624b3cd..a786ef7a1b9 100644 Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/IntervalTest.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/IntervalTest.vcf.idx differ diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/convertToBasePairResolution.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/convertToBasePairResolution.vcf index 85110d1b563..33ee7d30512 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/convertToBasePairResolution.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/convertToBasePairResolution.vcf @@ -8,20 +8,113 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine.CombineGVCFs= +##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) +##INFO= +##INFO= +##INFO= ##INFO= ##INFO= ##INFO= ##INFO= +##INFO= +##INFO= ##INFO= +##INFO= ##INFO= ##INFO= ##INFO= +##INFO= ##INFO= -##contig= -##contig= -##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +##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:///Users/ebanks/Sting_unstable/../references/hs37d5.fasta +##source=CombineGVCFs ##source=SelectVariants #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA1 NA2 20 69491 . G . . . GT:DP:GQ:MIN_DP:MIN_GQ:PL ./.:94:99:82:99:0,120,1800 ./. diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/convertToBasePairResolution.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/convertToBasePairResolution.vcf.idx index f277fbe0f3f..c62686ee4f6 100644 Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/convertToBasePairResolution.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/convertToBasePairResolution.vcf.idx differ 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 0cd93e453c5..e7d6dd0b7c3 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 @@ -8,7 +8,7 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine= +##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) ##INFO= ##INFO= @@ -25,7 +25,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##contig= 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 a041b98c6d9..a34a917aeb8 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 @@ -8,7 +8,7 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine= +##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) ##INFO= ##INFO= @@ -25,7 +25,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##contig= 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 439c67ecb33..0efbdb4898a 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 @@ -11,7 +11,7 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine= +##GATKCommandLine= ##GATKCommandLine= ##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive) ##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive) @@ -1508,24 +1508,24 @@ 20 10008944 . T . . . GT:DP:GQ:MIN_DP:PL ./.:47:78:47:0,78,1170 ./.:38:33:38:0,33,495 20 10008945 . A . . END=10008946 GT:DP:GQ:MIN_DP:PL ./.:47:81:46:0,81,1215 ./.:38:30:38:0,30,450 20 10008947 . T . . . GT:DP:GQ:MIN_DP:PL ./.:47:81:46:0,81,1215 ./.:38:0:38:0,0,894 -20 10008948 . TA T, . . BaseQRankSum=0.994;DP=85;ExcessHet=3.01;MQRankSum=2.05;RAW_MQandDP=256423,85;ReadPosRankSum=0.884 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:1,50,0:51:99:0|1:10008921_C_CA:2095,107,0,2098,159,2150:10008921:1,0,35,15 ./.:0,33,0:33:99:.:.:1406,99,0,1406,99,1406:.:0,0,15,18 -20 10008949 . A *, . . DP=85 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:1,50,0:51:99:0|1:10008921_C_CA:2095,107,0,2098,159,2150:10008921:1,0,35,15 ./.:0,33,0:33:99:.:.:1406,99,0,1406,99,1406:.:0,0,15,18 +20 10008948 . TA T, . . BaseQRankSum=0.994;DP=85;ExcessHet=3.01;MQRankSum=2.05;RAW_MQandDP=256423,85;ReadPosRankSum=0.884 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:1,50,0:51:99:0|1:10008921_C_CA:2105,117,0,2108,159,2150:10008921:1,0,35,15 ./.:0,33,0:33:99:.:.:1406,99,0,1406,99,1406:.:0,0,15,18 +20 10008949 . A *, . . DP=85 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:1,50,0:51:99:0|1:10008921_C_CA:2105,117,0,2108,159,2150:10008921:1,0,35,15 ./.:0,33,0:33:99:.:.:1406,99,0,1406,99,1406:.:0,0,15,18 20 10008950 . A . . . GT:DP:GQ:MIN_DP:PL ./.:52:99:52:0,99,1485 ./.:39:0:39:0,0,0 20 10008951 . A . . . GT:DP:GQ:MIN_DP:PL ./.:51:93:51:0,93,1395 ./.:39:0:39:0,0,0 -20 10008952 . CACACACACACACA C,CCA,CCACACACACA,CCACACACACACA,CCACA, . . BaseQRankSum=0.941;DP=95;ExcessHet=3.01;MQRankSum=1.84;RAW_MQandDP=282669,95;ReadPosRankSum=0.716 GT:AD:DP:GQ:PL:SB ./.:1,3,14,5,11,0,0:34:99:1704,876,1258,525,811,845,726,514,173,703,582,342,0,443,530,1135,1092,744,779,607,1321,1135,1092,744,779,607,1321,1321:1,0,25,8 ./.:0,0,0,15,0,12,0:27:99:1315,1243,1282,1243,1282,1282,505,512,512,439,1243,1282,1282,512,1282,648,714,714,0,714,719,1243,1282,1282,512,1282,714,1282:0,0,12,15 -20 10008953 . A *, . . DP=95 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1704,582,530,1135,607,1321:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 -20 10008954 . C *, . . DP=95 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1704,582,530,1135,607,1321:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 -20 10008955 . A *, . . DP=95 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1704,582,530,1135,607,1321:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 -20 10008956 . C *, . . DP=95 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1704,582,530,1135,607,1321:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 -20 10008957 . A *, . . DP=95 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1704,582,530,1135,607,1321:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 -20 10008958 . C *, . . DP=95 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1704,582,530,1135,607,1321:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 -20 10008959 . A *, . . DP=95 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1704,582,530,1135,607,1321:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 -20 10008960 . C *, . . DP=95 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1704,582,530,1135,607,1321:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 -20 10008961 . A *, . . DP=95 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1704,582,530,1135,607,1321:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 -20 10008962 . C *, . . DP=98 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:1,11,0:34:99:.:1704,582,530,1135,607,1321:1,0,25,8 ./.:.:39:82:39:0,82,1154,82,1154,1154 -20 10008963 . A *, . . DP=98 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:1,11,0:34:99:.:1704,582,530,1135,607,1321:1,0,25,8 ./.:.:39:82:39:0,82,1154,82,1154,1154 -20 10008964 . C *, . . DP=99 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:1,11,0:34:99:.:1704,582,530,1135,607,1321:1,0,25,8 ./.:.:42:99:40:0,99,1485,99,1485,1485 -20 10008965 . A *, . . DP=99 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:1,11,0:34:99:.:1704,582,530,1135,607,1321:1,0,25,8 ./.:.:42:99:40:0,99,1485,99,1485,1485 +20 10008952 . CACACACACACACA C,CCA,CCACACACACA,CCACACACACACA,CCACA, . . BaseQRankSum=0.941;DP=95;ExcessHet=3.01;MQRankSum=1.84;RAW_MQandDP=282669,95;ReadPosRankSum=0.716 GT:AD:DP:GQ:PL:SB ./.:1,3,14,5,11,0,0:34:99:1717,890,1216,539,769,803,739,496,154,687,596,342,0,443,533,1149,1060,712,761,607,1292,1149,1060,712,761,607,1292,1292:1,0,25,8 ./.:0,0,0,15,0,12,0:27:99:1315,1243,1282,1243,1282,1282,505,512,512,439,1243,1282,1282,512,1282,648,714,714,0,714,719,1243,1282,1282,512,1282,714,1282:0,0,12,15 +20 10008953 . A *, . . DP=95 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1717,596,533,1149,607,1292:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 +20 10008954 . C *, . . DP=95 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1717,596,533,1149,607,1292:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 +20 10008955 . A *, . . DP=95 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1717,596,533,1149,607,1292:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 +20 10008956 . C *, . . DP=95 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1717,596,533,1149,607,1292:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 +20 10008957 . A *, . . DP=95 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1717,596,533,1149,607,1292:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 +20 10008958 . C *, . . DP=95 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1717,596,533,1149,607,1292:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 +20 10008959 . A *, . . DP=95 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1717,596,533,1149,607,1292:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 +20 10008960 . C *, . . DP=95 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1717,596,533,1149,607,1292:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 +20 10008961 . A *, . . DP=95 GT:AD:DP:GQ:PL:SB ./.:1,11,0:34:99:1717,596,533,1149,607,1292:1,0,25,8 ./.:0,15,0:27:99:1315,505,439,1243,512,1282:0,0,12,15 +20 10008962 . C *, . . DP=98 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:1,11,0:34:99:.:1717,596,533,1149,607,1292:1,0,25,8 ./.:.:39:82:39:0,82,1154,82,1154,1154 +20 10008963 . A *, . . DP=98 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:1,11,0:34:99:.:1717,596,533,1149,607,1292:1,0,25,8 ./.:.:39:82:39:0,82,1154,82,1154,1154 +20 10008964 . C *, . . DP=99 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:1,11,0:34:99:.:1717,596,533,1149,607,1292:1,0,25,8 ./.:.:42:99:40:0,99,1485,99,1485,1485 +20 10008965 . A *, . . DP=99 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:1,11,0:34:99:.:1717,596,533,1149,607,1292:1,0,25,8 ./.:.:42:99:40:0,99,1485,99,1485,1485 20 10008966 . C . . END=10008979 GT:DP:GQ:MIN_DP:PL ./.:58:99:56:0,120,1800 ./.:42:99:40:0,99,1485 20 10008980 . C . . . GT:DP:GQ:MIN_DP:PL ./.:58:99:56:0,120,1800 ./.:43:95:43:0,95,1276 20 10008981 . A . . END=10008986 GT:DP:GQ:MIN_DP:PL ./.:58:99:56:0,120,1800 ./.:44:99:42:0,99,1342 @@ -3626,7 +3626,7 @@ 20 10027228 . G . . END=10027229 GT:DP:GQ:MIN_DP:PL ./.:70:99:52:0,115,1800 ./.:44:15:43:0,15,225 20 10027230 . A . . END=10027231 GT:DP:GQ:MIN_DP:PL ./.:70:99:52:0,115,1800 ./.:45:9:44:0,9,135 20 10027232 . A . . END=10027233 GT:DP:GQ:MIN_DP:PL ./.:70:99:52:0,115,1800 ./.:46:12:45:0,12,180 -20 10027234 . A ATTAG, . . BaseQRankSum=-4.060e-01;ClippingRankSum=0.00;DP=113;ExcessHet=3.01;MQRankSum=0.375;RAW_MQandDP=388151,113;ReadPosRankSum=0.211 GT:AD:DP:GQ:PL:SB ./.:34,35,0:69:99:1358,0,1964,1461,2069,3531:18,16,15,20 ./.:1,40,0:41:65:1767,65,0,1770,126,1832:0,1,19,21 +20 10027234 . A ATTAG, . . BaseQRankSum=-4.060e-01;ClippingRankSum=0.00;DP=113;ExcessHet=3.01;MQRankSum=0.375;RAW_MQandDP=388151,113;ReadPosRankSum=0.211 GT:AD:DP:GQ:PL:SB ./.:34,35,0:69:99:1358,0,1320,1461,1426,2887:18,16,15,20 ./.:1,40,0:41:65:1767,65,0,1770,126,1832:0,1,19,21 20 10027235 . T . . . GT:DP:GQ:MIN_DP:PL ./.:78:99:56:0,120,1800 ./.:45:0:45:0,0,0 20 10027236 . T . . END=10027304 GT:DP:GQ:MIN_DP:PL ./.:78:99:56:0,120,1800 ./.:45:99:41:0,114,1710 20 10027305 . A . . . GT:DP:GQ:MIN_DP:PL ./.:78:99:56:0,120,1800 ./.:47:97:47:0,97,1267 @@ -3645,9 +3645,9 @@ 20 10027555 . C . . END=10027801 GT:DP:GQ:MIN_DP:PL ./.:78:99:56:0,120,1800 ./.:49:99:36:0,100,1146 20 10027802 . A . . . GT:DP:GQ:MIN_DP:PL ./.:78:99:56:0,120,1800 ./.:41:88:41:0,88,1215 20 10027803 . T . . END=10027867 GT:DP:GQ:MIN_DP:PL ./.:78:99:56:0,120,1800 ./.:50:99:42:0,115,1296 -20 10027868 . A G, . . BaseQRankSum=-4.141e+00;ClippingRankSum=0.00;DP=134;ExcessHet=3.01;MQRankSum=0.032;RAW_MQandDP=476882,134;ReadPosRankSum=1.87 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:44,45,0:89:99:0|1:10027868_A_G:1768,0,3201,1901,3340,5240:10027868:19,25,26,19 ./.:19,24,0:43:99:0|1:10027868_A_G:927,0,1091,984,1164,2148:10027868:10,9,14,10 +20 10027868 . A G, . . BaseQRankSum=-4.141e+00;ClippingRankSum=0.00;DP=134;ExcessHet=3.01;MQRankSum=0.032;RAW_MQandDP=476882,134;ReadPosRankSum=1.87 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:44,45,0:89:99:0|1:10027868_A_G:1768,0,1671,1901,1810,3710:10027868:19,25,26,19 ./.:19,24,0:43:99:0|1:10027868_A_G:927,0,1091,984,1164,2148:10027868:10,9,14,10 20 10027869 . A . . END=10027871 GT:DP:GQ:MIN_DP:PL ./.:86:99:85:0,120,1800 ./.:48:99:46:0,120,1800 -20 10027872 . A G, . . BaseQRankSum=-8.550e-01;ClippingRankSum=0.00;DP=129;ExcessHet=3.01;MQRankSum=0.101;RAW_MQandDP=458882,129;ReadPosRankSum=1.05 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:40,45,0:85:99:0|1:10027868_A_G:1753,0,3136,1879,3272,5151:10027868:16,24,26,19 ./.:18,24,0:42:99:0|1:10027868_A_G:927,0,1091,984,1164,2148:10027868:9,9,14,10 +20 10027872 . A G, . . BaseQRankSum=-8.550e-01;ClippingRankSum=0.00;DP=129;ExcessHet=3.01;MQRankSum=0.101;RAW_MQandDP=458882,129;ReadPosRankSum=1.05 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:40,45,0:85:99:0|1:10027868_A_G:1753,0,1606,1879,1742,3621:10027868:16,24,26,19 ./.:18,24,0:42:99:0|1:10027868_A_G:927,0,1091,984,1164,2148:10027868:9,9,14,10 20 10027873 . G . . END=10027989 GT:DP:GQ:MIN_DP:PL ./.:80:99:55:0,120,1800 ./.:45:99:41:0,105,1244 20 10027990 . C . . . GT:DP:GQ:MIN_DP:PL ./.:80:99:55:0,120,1800 ./.:42:75:42:0,75,1081 20 10027991 . G . . END=10028073 GT:DP:GQ:MIN_DP:PL ./.:80:99:55:0,120,1800 ./.:45:99:38:0,103,1137 @@ -4104,7 +4104,7 @@ 20 10032959 . T . . END=10032961 GT:DP:GQ:MIN_DP:PL ./.:67:99:61:0,120,1800 ./.:45:12:45:0,12,180 20 10032962 . G . . . GT:DP:GQ:MIN_DP:PL ./.:67:99:61:0,120,1800 ./.:46:6:46:0,6,90 20 10032963 . C . . END=10032971 GT:DP:GQ:MIN_DP:PL ./.:67:99:61:0,120,1800 ./.:45:0:44:0,0,0 -20 10032972 . C CAT, . . BaseQRankSum=-3.540e-01;DP=109;ExcessHet=3.01;MQRankSum=-1.017e+00;RAW_MQandDP=390941,109;ReadPosRankSum=-1.232e+00 GT:AD:DP:GQ:PL:SB ./.:33,30,0:63:99:1160,0,1477,1260,1568,2827:17,16,11,19 ./.:0,43,0:43:99:1944,132,0,1944,132,1944:0,0,21,22 +20 10032972 . C CAT, . . BaseQRankSum=-3.540e-01;DP=109;ExcessHet=3.01;MQRankSum=-1.017e+00;RAW_MQandDP=390941,109;ReadPosRankSum=-1.232e+00 GT:AD:DP:GQ:PL:SB ./.:33,30,0:63:99:1160,0,1295,1260,1386,2645:17,16,11,19 ./.:0,43,0:43:99:1944,132,0,1944,132,1944:0,0,21,22 20 10032973 . T . . . GT:DP:GQ:MIN_DP:PL ./.:78:99:50:0,120,1800 ./.:43:0:43:0,0,0 20 10032974 . G . . . GT:DP:GQ:MIN_DP:PL ./.:78:99:50:0,120,1800 ./.:44:96:44:0,96,1179 20 10032975 . A . . END=10033031 GT:DP:GQ:MIN_DP:PL ./.:78:99:50:0,120,1800 ./.:42:99:36:0,99,1093 @@ -4423,27 +4423,27 @@ 20 10036915 . T . . END=10036925 GT:DP:GQ:MIN_DP:PL ./.:76:99:43:0,113,1513 ./.:29:75:28:0,75,1125 20 10036926 . A . . . GT:DP:GQ:MIN_DP:PL ./.:76:99:43:0,113,1513 ./.:29:81:29:0,81,1215 20 10036927 . G . . END=10036929 GT:DP:GQ:MIN_DP:PL ./.:76:99:43:0,113,1513 ./.:29:78:27:0,78,1170 -20 10036930 . CGATAGCCCTAGCCCTAGATA C, . . BaseQRankSum=0.200;ClippingRankSum=0.00;DP=129;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=404447,129;ReadPosRankSum=0.460 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 -20 10036931 . G *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 -20 10036932 . A *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 -20 10036933 . T *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 -20 10036934 . A *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 -20 10036935 . G *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 -20 10036936 . C *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 -20 10036937 . C *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 -20 10036938 . C *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 -20 10036939 . T *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 -20 10036940 . A *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 -20 10036941 . G *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 -20 10036942 . C *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 -20 10036943 . C *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 -20 10036944 . C *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 -20 10036945 . T *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 -20 10036946 . A *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 -20 10036947 . G *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 -20 10036948 . A *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 -20 10036949 . T *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 -20 10036950 . A *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,5571,1191,5665,6856:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036930 . CGATAGCCCTAGCCCTAGATA C, . . BaseQRankSum=0.200;ClippingRankSum=0.00;DP=129;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=404447,129;ReadPosRankSum=0.460 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036931 . G *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036932 . A *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036933 . T *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036934 . A *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036935 . G *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036936 . C *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036937 . C *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036938 . C *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036939 . T *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036940 . A *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036941 . G *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036942 . C *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036943 . C *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036944 . C *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036945 . T *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036946 . A *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036947 . G *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036948 . A *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036949 . T *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 +20 10036950 . A *, . . DP=129 GT:AD:DP:GQ:PL:SB ./.:39,29,0:68:99:1074,0,1505,1191,1599,2790:11,28,15,14 ./.:20,13,0:33:99:487,0,3108,547,3148,3695:8,12,6,7 20 10036951 . G . . . GT:DP:GQ:MIN_DP:PL ./.:74:99:70:0,120,1800 ./.:33:0:33:0,0,569 20 10036952 . A . . END=10036956 GT:DP:GQ:MIN_DP:PL ./.:74:99:70:0,120,1800 ./.:33:90:33:0,90,1059 20 10036957 . C . . . GT:DP:GQ:MIN_DP:PL ./.:70:37:70:0,37,2472 ./.:35:37:35:0,37,931 @@ -5040,7 +5040,7 @@ 20 10042968 . A . . END=10042980 GT:DP:GQ:MIN_DP:PL ./.:65:99:56:0,120,1800 ./.:43:99:36:0,108,1088 20 10042981 . C . . . GT:DP:GQ:MIN_DP:PL ./.:65:99:56:0,120,1800 ./.:43:96:43:0,96,1172 20 10042982 . C . . END=10043001 GT:DP:GQ:MIN_DP:PL ./.:65:99:56:0,120,1800 ./.:42:99:40:0,109,1146 -20 10043002 . A T, . . BaseQRankSum=3.99;DP=126;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=309600,86;ReadPosRankSum=-3.500e-02 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:48,38,0:86:99:.:1316,0,1659,1460,1773,3233:19,29,18,20 ./.:.:42:99:40:0,109,1146,109,1146,1146 +20 10043002 . A T, . . BaseQRankSum=3.99;DP=126;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=309600,86;ReadPosRankSum=-3.500e-02 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:48,38,0:86:99:.:1316,0,1658,1460,1772,3232:19,29,18,20 ./.:.:42:99:40:0,109,1146,109,1146,1146 20 10043003 . C . . END=10043005 GT:DP:GQ:MIN_DP:PL ./.:78:99:44:0,104,1655 ./.:42:99:40:0,109,1146 20 10043006 . C . . . GT:DP:GQ:MIN_DP:PL ./.:78:99:44:0,104,1655 ./.:42:95:42:0,95,1202 20 10043007 . T . . END=10043164 GT:DP:GQ:MIN_DP:PL ./.:78:99:44:0,104,1655 ./.:52:99:41:0,102,1381 @@ -8869,9 +8869,9 @@ 20 10076996 . A . . END=10076998 GT:DP:GQ:MIN_DP:PL ./.:69:99:59:0,120,1800 ./.:36:81:36:0,81,1215 20 10076999 . A . . END=10077000 GT:DP:GQ:MIN_DP:PL ./.:69:99:59:0,120,1800 ./.:36:75:36:0,75,1125 20 10077001 . A . . END=10077007 GT:DP:GQ:MIN_DP:PL ./.:69:99:59:0,120,1800 ./.:38:81:38:0,81,1215 -20 10077008 . T A, . . BaseQRankSum=-1.748e+00;ClippingRankSum=0.00;DP=79;ExcessHet=3.01;MQRankSum=0.725;RAW_MQandDP=270123,79;ReadPosRankSum=0.805 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:46,4,0:50:42:0|1:10077008_T_A:0,42,2066,148,2078,2184:10077008:18,28,4,0 ./.:23,3,0:26:7:0|1:10076989_C_CAAAA:0,7,855,69,864,926:10076989:11,12,3,0 +20 10077008 . T A, . . BaseQRankSum=-1.748e+00;ClippingRankSum=0.00;DP=79;ExcessHet=3.01;MQRankSum=0.725;RAW_MQandDP=270123,79;ReadPosRankSum=0.805 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:46,4,0:50:42:0|1:10077008_T_A:0,42,1971,148,1983,2089:10077008:18,28,4,0 ./.:23,3,0:26:7:0|1:10076989_C_CAAAA:0,7,855,69,864,926:10076989:11,12,3,0 20 10077009 . A . . . GT:DP:GQ:MIN_DP:PL ./.:52:99:52:0,120,1800 ./.:36:78:36:0,78,1170 -20 10077010 . G A, . . BaseQRankSum=-1.841e+00;ClippingRankSum=0.00;DP=78;ExcessHet=3.01;MQRankSum=0.558;RAW_MQandDP=268523,78;ReadPosRankSum=0.911 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:48,4,0:52:42:0|1:10077008_T_A:0,42,2066,148,2078,2184:10077008:18,30,4,0 ./.:21,2,0:23:7:0|1:10076989_C_CAAAA:0,7,855,69,864,925:10076989:10,11,2,0 +20 10077010 . G A, . . BaseQRankSum=-1.841e+00;ClippingRankSum=0.00;DP=78;ExcessHet=3.01;MQRankSum=0.558;RAW_MQandDP=268523,78;ReadPosRankSum=0.911 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:48,4,0:52:42:0|1:10077008_T_A:0,42,1971,148,1983,2089:10077008:18,30,4,0 ./.:21,2,0:23:7:0|1:10076989_C_CAAAA:0,7,855,69,864,925:10076989:10,11,2,0 20 10077011 . A . . END=10077012 GT:DP:GQ:MIN_DP:PL ./.:69:99:44:0,102,1654 ./.:33:78:33:0,78,1170 20 10077013 . A . . . GT:DP:GQ:MIN_DP:PL ./.:69:99:44:0,102,1654 ./.:33:81:33:0,81,1215 20 10077014 . A . . . GT:DP:GQ:MIN_DP:PL ./.:69:99:44:0,102,1654 ./.:32:71:32:0,71,971 @@ -10165,14 +10165,14 @@ 20 10088964 . G . . . GT:DP:GQ:MIN_DP:PL ./.:49:99:42:0,110,1709 ./.:37:30:37:0,30,450 20 10088965 . T . . . GT:DP:GQ:MIN_DP:PL ./.:49:99:42:0,110,1709 ./.:41:27:41:0,27,405 20 10088966 . C . . END=10088967 GT:DP:GQ:MIN_DP:PL ./.:49:99:42:0,110,1709 ./.:42:0:41:0,0,683 -20 10088968 . C CAAA, . . BaseQRankSum=0.552;DP=95;ExcessHet=3.01;MQRankSum=-4.750e+00;RAW_MQandDP=292450,95;ReadPosRankSum=2.42 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:30,23,0:53:99:0|1:10088968_C_CAAA:1213,0,1367,1310,1463,2773:10088968:16,14,14,9 ./.:0,30,0:30:99:0|1:10088968_C_CAAA:1781,128,0,1781,128,1781:10088968:0,0,18,12 +20 10088968 . C CAAA, . . BaseQRankSum=0.552;DP=95;ExcessHet=3.01;MQRankSum=-4.750e+00;RAW_MQandDP=292450,95;ReadPosRankSum=2.42 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:30,23,0:53:99:0|1:10088968_C_CAAA:1213,0,1236,1310,1333,2642:10088968:16,14,14,9 ./.:0,30,0:30:99:0|1:10088968_C_CAAA:1781,128,0,1781,128,1781:10088968:0,0,18,12 20 10088969 . A . . . GT:DP:GQ:MIN_DP:PL ./.:71:99:70:0,120,1800 ./.:53:0:53:0,0,0 20 10088970 . A . . END=10088979 GT:DP:GQ:MIN_DP:PL ./.:71:99:70:0,120,1800 ./.:54:99:53:0,120,1800 -20 10088980 . T C, . . BaseQRankSum=-1.585e+00;DP=113;ExcessHet=3.01;MQRankSum=-5.232e+00;RAW_MQandDP=332195,113;ReadPosRankSum=1.29 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:37,31,0:68:99:0|1:10088968_C_CAAA:1276,0,1627,1394,1729,3123:10088968:19,18,15,16 ./.:0,44,0:44:99:0|1:10088968_C_CAAA:1859,135,0,1859,135,1859:10088968:0,0,18,26 +20 10088980 . T C, . . BaseQRankSum=-1.585e+00;DP=113;ExcessHet=3.01;MQRankSum=-5.232e+00;RAW_MQandDP=332195,113;ReadPosRankSum=1.29 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:37,31,0:68:99:0|1:10088968_C_CAAA:1276,0,1497,1394,1599,2993:10088968:19,18,15,16 ./.:0,44,0:44:99:0|1:10088968_C_CAAA:1859,135,0,1859,135,1859:10088968:0,0,18,26 20 10088981 . A . . END=10088982 GT:DP:GQ:MIN_DP:PL ./.:71:99:69:0,120,1800 ./.:54:99:54:0,120,1800 20 10088983 . A . . . GT:DP:GQ:MIN_DP:PL ./.:71:99:69:0,120,1800 ./.:51:43:51:0,43,1358 20 10088984 . A . . . GT:DP:GQ:MIN_DP:PL ./.:71:99:69:0,120,1800 ./.:53:99:53:0,120,1800 -20 10088985 . T C, . . BaseQRankSum=-1.920e-01;DP=118;ExcessHet=3.01;MQRankSum=-5.248e+00;RAW_MQandDP=346085,118;ReadPosRankSum=1.23 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:42,32,0:74:99:0|1:10088968_C_CAAA:1207,0,1729,1333,1826,3159:10088968:22,20,15,17 ./.:0,43,0:43:99:.:.:1926,132,0,1926,132,1926:.:0,0,18,25 +20 10088985 . T C, . . BaseQRankSum=-1.920e-01;DP=118;ExcessHet=3.01;MQRankSum=-5.248e+00;RAW_MQandDP=346085,118;ReadPosRankSum=1.23 GT:AD:DP:GQ:PGT:PID:PL:PS:SB .|.:42,32,0:74:99:0|1:10088968_C_CAAA:1207,0,1599,1333,1695,3029:10088968:22,20,15,17 ./.:0,43,0:43:99:.:.:1926,132,0,1926,132,1926:.:0,0,18,25 20 10088986 . A . . END=10088989 GT:DP:GQ:MIN_DP:PL ./.:82:99:81:0,120,1800 ./.:52:99:49:0,110,1473 20 10088990 . A . . . GT:DP:GQ:MIN_DP:PL ./.:84:7:84:0,7,2771 ./.:52:99:49:0,110,1473 20 10088991 . C . . . GT:DP:GQ:MIN_DP:PL ./.:81:95:81:0,95,2703 ./.:52:99:49:0,110,1473 @@ -10401,7 +10401,7 @@ 20 10092262 . A . . END=10092288 GT:DP:GQ:MIN_DP:PL ./.:69:99:46:0,120,1800 ./.:41:99:38:0,102,1110 20 10092289 . G . . . GT:DP:GQ:MIN_DP:PL ./.:69:99:46:0,120,1800 ./.:43:97:43:0,97,1263 20 10092290 . T . . END=10092414 GT:DP:GQ:MIN_DP:PL ./.:69:99:46:0,120,1800 ./.:54:99:39:0,108,1239 -20 10092415 . A G, . . BaseQRankSum=-6.731e+00;DP=140;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=363600,101;ReadPosRankSum=0.082 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:52,49,0:101:99:.:1664,0,1902,1820,2049,3870:27,25,24,25 ./.:.:54:99:39:0,108,1239,108,1239,1239 +20 10092415 . A G, . . BaseQRankSum=-6.731e+00;DP=140;ExcessHet=3.01;MQRankSum=0.00;RAW_MQandDP=363600,101;ReadPosRankSum=0.082 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:52,49,0:101:99:.:1664,0,1901,1820,2049,3869:27,25,24,25 ./.:.:54:99:39:0,108,1239,108,1239,1239 20 10092416 . G . . END=10092641 GT:DP:GQ:MIN_DP:PL ./.:80:99:60:0,120,1800 ./.:54:99:39:0,108,1239 20 10092642 . T C, . . DP=111;ExcessHet=3.01;RAW_MQandDP=183600,51 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:.:80:99:60:0,120,1800,120,1800,1800 ./.:0,51,0:51:99:.:1428,151,0,1428,151,1428:0,0,26,25 20 10092643 . G . . END=10092926 GT:DP:GQ:MIN_DP:PL ./.:80:99:60:0,120,1800 ./.:57:99:40:0,108,1608 @@ -10668,16 +10668,16 @@ 20 10095429 . C . . . GT:DP:GQ:MIN_DP:PL ./.:77:99:63:0,120,1800 ./.:41:21:41:0,21,315 20 10095430 . A . . . GT:DP:GQ:MIN_DP:PL ./.:77:99:63:0,120,1800 ./.:40:18:40:0,18,270 20 10095431 . A . . . GT:DP:GQ:MIN_DP:PL ./.:77:99:63:0,120,1800 ./.:39:15:39:0,15,225 -20 10095432 . GTGATGATGA GTGA,G, . . BaseQRankSum=1.27;DP=112;ExcessHet=3.01;MQRankSum=-4.431e+00;RAW_MQandDP=353748,112;ReadPosRankSum=0.396 GT:AD:DP:GQ:PL:SB ./.:27,0,23,0:50:99:877,959,3140,0,2181,2108,959,3140,2181,3140:16,11,12,11 ./.:0,27,0,0:27:82:1217,82,0,1217,82,1217,1217,82,1217,1217:0,0,13,14 -20 10095433 . T *, . . DP=112 GT:AD:DP:GQ:PL:SB ./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11 ./.:0,27,0:27:82:1217,82,0,1217,82,1217:0,0,13,14 -20 10095434 . G *, . . DP=112 GT:AD:DP:GQ:PL:SB ./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11 ./.:0,27,0:27:82:1217,82,0,1217,82,1217:0,0,13,14 -20 10095435 . A *, . . DP=112 GT:AD:DP:GQ:PL:SB ./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11 ./.:0,27,0:27:82:1217,82,0,1217,82,1217:0,0,13,14 -20 10095436 . T *, . . DP=112 GT:AD:DP:GQ:PL:SB ./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11 ./.:0,27,0:27:82:1217,82,0,1217,82,1217:0,0,13,14 -20 10095437 . G *, . . DP=112 GT:AD:DP:GQ:PL:SB ./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11 ./.:0,27,0:27:82:1217,82,0,1217,82,1217:0,0,13,14 -20 10095438 . A *, . . DP=112 GT:AD:DP:GQ:PL:SB ./.:27,23,0:50:99:877,0,2108,959,2181,3140:16,11,12,11 ./.:0,27,0:27:82:1217,82,0,1217,82,1217:0,0,13,14 -20 10095439 . T *, . . DP=113 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:27,23,0:50:99:.:877,0,2108,959,2181,3140:16,11,12,11 ./.:.:36:0:36:0,0,0,0,0,0 -20 10095440 . G *, . . DP=109 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:27,23,0:50:99:.:877,0,2108,959,2181,3140:16,11,12,11 ./.:.:35:90:32:0,90,1021,90,1021,1021 -20 10095441 . A *, . . DP=109 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:27,23,0:50:99:.:877,0,2108,959,2181,3140:16,11,12,11 ./.:.:35:90:32:0,90,1021,90,1021,1021 +20 10095432 . GTGATGATGA GTGA,G, . . BaseQRankSum=1.27;DP=112;ExcessHet=3.01;MQRankSum=-4.431e+00;RAW_MQandDP=353748,112;ReadPosRankSum=0.396 GT:AD:DP:GQ:PL:SB ./.:27,0,23,0:50:99:877,959,2030,0,1071,998,959,2030,1071,2030:16,11,12,11 ./.:0,27,0,0:27:82:1217,82,0,1217,82,1217,1217,82,1217,1217:0,0,13,14 +20 10095433 . T *, . . DP=112 GT:AD:DP:GQ:PL:SB ./.:27,23,0:50:99:877,0,998,959,1071,2030:16,11,12,11 ./.:0,27,0:27:82:1217,82,0,1217,82,1217:0,0,13,14 +20 10095434 . G *, . . DP=112 GT:AD:DP:GQ:PL:SB ./.:27,23,0:50:99:877,0,998,959,1071,2030:16,11,12,11 ./.:0,27,0:27:82:1217,82,0,1217,82,1217:0,0,13,14 +20 10095435 . A *, . . DP=112 GT:AD:DP:GQ:PL:SB ./.:27,23,0:50:99:877,0,998,959,1071,2030:16,11,12,11 ./.:0,27,0:27:82:1217,82,0,1217,82,1217:0,0,13,14 +20 10095436 . T *, . . DP=112 GT:AD:DP:GQ:PL:SB ./.:27,23,0:50:99:877,0,998,959,1071,2030:16,11,12,11 ./.:0,27,0:27:82:1217,82,0,1217,82,1217:0,0,13,14 +20 10095437 . G *, . . DP=112 GT:AD:DP:GQ:PL:SB ./.:27,23,0:50:99:877,0,998,959,1071,2030:16,11,12,11 ./.:0,27,0:27:82:1217,82,0,1217,82,1217:0,0,13,14 +20 10095438 . A *, . . DP=112 GT:AD:DP:GQ:PL:SB ./.:27,23,0:50:99:877,0,998,959,1071,2030:16,11,12,11 ./.:0,27,0:27:82:1217,82,0,1217,82,1217:0,0,13,14 +20 10095439 . T *, . . DP=113 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:27,23,0:50:99:.:877,0,998,959,1071,2030:16,11,12,11 ./.:.:36:0:36:0,0,0,0,0,0 +20 10095440 . G *, . . DP=109 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:27,23,0:50:99:.:877,0,998,959,1071,2030:16,11,12,11 ./.:.:35:90:32:0,90,1021,90,1021,1021 +20 10095441 . A *, . . DP=109 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:27,23,0:50:99:.:877,0,998,959,1071,2030:16,11,12,11 ./.:.:35:90:32:0,90,1021,90,1021,1021 20 10095442 . T . . END=10095468 GT:DP:GQ:MIN_DP:PL ./.:80:99:64:0,120,1800 ./.:35:90:32:0,90,1021 20 10095469 . T . . END=10095472 GT:DP:GQ:MIN_DP:PL ./.:80:99:64:0,120,1800 ./.:33:99:33:0,99,1037 20 10095473 . G . . . GT:DP:GQ:MIN_DP:PL ./.:80:99:64:0,120,1800 ./.:33:54:33:0,54,948 @@ -10833,7 +10833,7 @@ 20 10097098 . A . . . GT:DP:GQ:MIN_DP:PL ./.:91:99:77:0,120,1800 ./.:36:24:36:0,24,360 20 10097099 . T . . . GT:DP:GQ:MIN_DP:PL ./.:91:99:77:0,120,1800 ./.:39:18:39:0,18,270 20 10097100 . T . . . GT:DP:GQ:MIN_DP:PL ./.:91:99:77:0,120,1800 ./.:39:21:39:0,21,315 -20 10097101 . C CTTTT,CTTT, . . BaseQRankSum=-1.134e+00;DP=104;ExcessHet=3.01;MQRankSum=-2.428e+00;RAW_MQandDP=353094,104;ReadPosRankSum=2.09 GT:AD:DP:GQ:PL:SB ./.:34,4,26,0:64:99:1129,558,2012,0,1324,1306,982,2052,1430,2377:22,12,15,15 ./.:0,22,0,0:22:71:1008,71,0,1008,71,1009,1008,71,1009,1009:0,0,13,9 +20 10097101 . C CTTTT,CTTT, . . BaseQRankSum=-1.134e+00;DP=104;ExcessHet=3.01;MQRankSum=-2.428e+00;RAW_MQandDP=353094,104;ReadPosRankSum=2.09 GT:AD:DP:GQ:PL:SB ./.:34,4,26,0:64:99:1129,558,1826,0,1242,1259,982,1910,1358,2261:22,12,15,15 ./.:0,22,0,0:22:71:1008,71,0,1008,71,1009,1008,71,1009,1009:0,0,13,9 20 10097102 . T . . . GT:DP:GQ:MIN_DP:PL ./.:70:99:60:0,120,1800 ./.:36:0:36:0,0,0 20 10097103 . T . . END=10097107 GT:DP:GQ:MIN_DP:PL ./.:70:99:60:0,120,1800 ./.:36:60:35:0,60,900 20 10097108 . T . . . GT:DP:GQ:MIN_DP:PL ./.:70:99:60:0,120,1800 ./.:36:72:36:0,72,1080 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf.idx index 4bcf94f43f4..631d726750e 100644 Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/newMQcalc.combined.g.vcf.idx differ diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionBaseExtensionTestExpected.g.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionBaseExtensionTestExpected.g.vcf index 5828cb041b8..bb097238f80 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionBaseExtensionTestExpected.g.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionBaseExtensionTestExpected.g.vcf @@ -8,7 +8,7 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine= +##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) ##INFO= ##INFO= @@ -25,7 +25,6 @@ ##INFO= ##INFO= ##INFO= -##INFO= ##INFO= ##INFO= ##contig= diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionRestrictToStartExpected.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionRestrictToStartExpected.vcf index c4c3715c61e..7f2911b1fe6 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionRestrictToStartExpected.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionRestrictToStartExpected.vcf @@ -8,13 +8,25 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine.CombineGVCFs= +##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) +##INFO= +##INFO= +##INFO= +##INFO= ##INFO= ##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= ##contig= ##contig= -##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +##source=CombineGVCFs #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA1 NA2 20 69491 . G . . END=69510 GT:DP:GQ:MIN_DP:MIN_GQ:PL ./.:94:99:82:99:0,120,1800 ./.:94:99:82:99:0,122,1802 20 69511 . ACAT A, . . DP=162 GT:AD:DP:GQ:MIN_DP:MIN_GQ:PL:SB ./.:1,79,0:80:99:.:.:2284,207,0,2287,237,2316:0,1,46,33 ./.:.:94:99:82:99:0,122,1802,122,1802,1802 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionRestrictToStartExpected.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionRestrictToStartExpected.vcf.idx index d0f104809af..9576322b9ec 100644 Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionRestrictToStartExpected.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/spanningDeletionRestrictToStartExpected.vcf.idx differ diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotations.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotations.vcf index a1955dd5b3d..87d983d3045 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotations.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotations.vcf @@ -10,8 +10,8 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine.CombineGVCFs= ##GATKCommandLine.HaplotypeCaller= +##GATKCommandLine= ##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive) ##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive) ##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive) @@ -77,31 +77,127 @@ ##GVCFBlock9-10=minGQ=9(inclusive),maxGQ=10(exclusive) ##GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive) ##GVCFBlock99-100=minGQ=99(inclusive),maxGQ=100(exclusive) +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= ##INFO= -##INFO= +##INFO= +##INFO= +##INFO= ##INFO= ##INFO= ##INFO= ##INFO= +##INFO= ##INFO= +##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= +##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= +##INFO= ##INFO= ##INFO= -##contig= -##contig= -##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +##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= +##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta +##source=CombineGVCFs #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA12892 -20 10087820 . CAG CAGAGAG,CAGAGAGAG,C,CAGAG, . . AS_RAW_BaseQRankSum=||1.0,1||-2.1,1|;AS_RAW_MQ=220977.00|4441.00|47258.00|3600.00|46800.00|0.00;AS_RAW_MQRankSum=||-3.1,1||0.6,1|;AS_RAW_ReadPosRankSum=||-0.3,1||-0.4,1|;AS_SB_TABLE=33,31|0,2|12,12|1,0|8,5|0,0;BaseQRankSum=0.955;DP=167;ExcessHet=3.01;MQRankSum=0.678;RAW_MQ=541599.00;ReadPosRankSum=-2.540e-01 GT:AD:GQ:PL:SB ./.:35,0,0,1,13,0:99:302,483,1922,483,1922,1922,490,1995,1995,2306,0,1169,1169,1170,1079,483,1922,1922,1995,1169,1922:17,18,9,5 ./.:29,2,24,0,0,0:99:606,627,1620,0,864,849,697,1597,927,1653,697,1597,927,1653,1653,697,1597,927,1653,1653,1653:16,13,12,14 +20 10087820 . CAG CAGAGAG,CAGAGAGAG,C,CAGAG, . . AS_RAW_BaseQRankSum=||1.0,1||-2.1,1|;AS_RAW_MQ=220977.00|4441.00|47258.00|3600.00|46800.00|0.00;AS_RAW_MQRankSum=||-3.1,1||0.6,1|;AS_RAW_ReadPosRankSum=||-0.3,1||-0.4,1|;AS_SB_TABLE=33,31|0,2|12,12|1,0|8,5|0,0;BaseQRankSum=0.955;DP=167;ExcessHet=3.01;MQRankSum=0.678;RAW_MQ=329810.00;ReadPosRankSum=-2.540e-01 GT:AD:GQ:PL:SB ./.:35,0,0,1,13,0:99:302,483,1922,483,1922,1922,490,1995,1995,2306,0,1169,1169,1170,1079,483,1922,1922,1995,1169,1922:17,18,9,5 ./.:29,2,24,0,0,0:99:606,627,1620,0,864,849,697,1597,927,1653,697,1597,927,1653,1653,697,1597,927,1653,1653,1653:16,13,12,14 20 10087821 . A *, . . DP=93 GT:AD:GQ:PL:SB ./.:35,1,0:99:302,490,2306,483,1995,1922:17,18,9,5 ./. 20 10087822 . G *, . . DP=93 GT:AD:GQ:PL:SB ./.:35,1,0:99:302,490,2306,483,1995,1922:17,18,9,5 ./. 20 10433000 . G . . END=10433048 GT:DP:GQ:MIN_DP:PL ./.:73:99:40:0,99,1485 ./.:50:99:43:0,102,1530 @@ -198,7 +294,7 @@ 20 10433308 . G . . . GT:DP:GQ:MIN_DP:PL ./.:27:18:27:0,18,270 ./.:34:21:34:0,21,315 20 10433309 . T . . . GT:DP:GQ:MIN_DP:PL ./.:27:12:27:0,12,180 ./.:35:6:35:0,6,90 20 10433310 . C . . END=10433311 GT:DP:GQ:MIN_DP:PL ./.:27:6:27:0,6,90 ./.:35:6:35:0,6,90 -20 10433312 . CAAAAAAA C,CAAAAAA, . . AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=76598.00|0.00|1682.00|0.00;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=19,20|0,0|1,1|0,0;BaseQRankSum=1.59;DP=80;ExcessHet=3.01;MQRankSum=-1.259e+00;RAW_MQ=179123.00;ReadPosRankSum=0.333 GT:AD:GQ:PL:SB ./.:16,0,0,0:48:0,74,1123,48,615,553,75,891,606,839:6,10,0,0 ./.:23,0,2,0:10:0,81,1139,10,811,747,81,1026,798,979:13,10,1,1 +20 10433312 . CAAAAAAA C,CAAAAAA, . . AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=76598.00|0.00|1682.00|0.00;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=19,20|0,0|1,1|0,0;BaseQRankSum=1.59;DP=80;ExcessHet=3.01;MQRankSum=-1.259e+00;RAW_MQ=95936.00;ReadPosRankSum=0.333 GT:AD:GQ:PL:SB ./.:16,0,0,0:48:0,74,1123,48,615,553,75,891,606,839:6,10,0,0 ./.:23,0,2,0:10:0,81,1139,10,811,747,81,1026,798,979:13,10,1,1 20 10433313 . A *, . . DP=80 GT:AD:GQ:PL:SB ./.:16,0,0:48:0,48,553,75,606,839:6,10,0,0 ./.:23,2,0:10:0,10,747,81,798,979:13,10,1,1 20 10433314 . A *, . . DP=80 GT:AD:GQ:PL:SB ./.:16,0,0:48:0,48,553,75,606,839:6,10,0,0 ./.:23,2,0:10:0,10,747,81,798,979:13,10,1,1 20 10433315 . A *, . . DP=80 GT:AD:GQ:PL:SB ./.:16,0,0:48:0,48,553,75,606,839:6,10,0,0 ./.:23,2,0:10:0,10,747,81,798,979:13,10,1,1 @@ -208,13 +304,13 @@ 20 10433319 . A *, . . DP=80 GT:AD:GQ:PL:SB ./.:16,0,0:48:0,48,553,75,606,839:6,10,0,0 ./.:23,2,0:10:0,10,747,81,798,979:13,10,1,1 20 10433320 . A . . . GT:DP:GQ:MIN_DP:PL ./.:25:0:25:0,0,708 ./.:34:0:34:0,0,1030 20 10433321 . A . . . GT:DP:GQ:MIN_DP:PL ./.:29:33:29:0,33,495 ./.:35:21:35:0,21,315 -20 10433322 . A AT,ATAT, . . AS_RAW_BaseQRankSum=|0.8,1,2.5,1||;AS_RAW_MQ=17782.00|41312.00|2523.00|0.00;AS_RAW_MQRankSum=|1.1,1,2.2,1||;AS_RAW_ReadPosRankSum=|1.9,1,2.0,1||;AS_SB_TABLE=7,8|8,9|2,1|0,0;BaseQRankSum=2.56;DP=77;ExcessHet=3.01;MQRankSum=1.90;RAW_MQ=154528.00;ReadPosRankSum=2.04 GT:AD:GQ:PL:SB ./.:11,5,0,0:99:124,0,369,158,384,542,158,384,542,542:5,6,2,3 ./.:4,12,3,0:19:450,0,46,298,19,576,442,117,506,617:2,2,8,7 +20 10433322 . A AT,ATAT, . . AS_RAW_BaseQRankSum=|0.8,1,2.5,1||;AS_RAW_MQ=17782.00|41312.00|2523.00|0.00;AS_RAW_MQRankSum=|1.1,1,2.2,1||;AS_RAW_ReadPosRankSum=|1.9,1,2.0,1||;AS_SB_TABLE=7,8|8,9|2,1|0,0;BaseQRankSum=2.56;DP=77;ExcessHet=3.01;MQRankSum=1.90;RAW_MQ=86818.00;ReadPosRankSum=2.04 GT:AD:GQ:PL:SB ./.:11,5,0,0:99:124,0,369,158,384,542,158,384,542,542:5,6,2,3 ./.:4,12,3,0:19:450,0,46,298,19,576,442,117,506,617:2,2,8,7 20 10433323 . A . . . GT:DP:GQ:MIN_DP:PL ./.:29:0:29:0,0,502 ./.:34:0:34:0,0,0 -20 10433324 . A T, . . AS_RAW_BaseQRankSum=|2.2,1|;AS_RAW_MQ=12736.00|48881.00|0.00;AS_RAW_MQRankSum=|0.5,1|;AS_RAW_ReadPosRankSum=|1.5,1|;AS_SB_TABLE=2,7|13,13|0,0;BaseQRankSum=2.28;DP=73;ExcessHet=3.01;MQRankSum=0.871;RAW_MQ=140128.00;ReadPosRankSum=1.74 GT:AD:GQ:PGT:PID:PL:SB ./.:8,6,0:99:0|1:10433324_A_T:228,0,275,252,294,546:2,6,2,4 ./.:1,20,0:53:0|1:10433324_A_T:877,53,0,880,61,888:0,1,11,9 +20 10433324 . A T, . . AS_RAW_BaseQRankSum=|2.2,1|;AS_RAW_MQ=12736.00|48881.00|0.00;AS_RAW_MQRankSum=|0.5,1|;AS_RAW_ReadPosRankSum=|1.5,1|;AS_SB_TABLE=2,7|13,13|0,0;BaseQRankSum=2.28;DP=73;ExcessHet=3.01;MQRankSum=0.871;RAW_MQ=79618.00;ReadPosRankSum=1.74 GT:AD:GQ:PGT:PID:PL:SB ./.:8,6,0:99:0|1:10433324_A_T:228,0,275,252,294,546:2,6,2,4 ./.:1,20,0:53:0|1:10433324_A_T:877,53,0,880,61,888:0,1,11,9 20 10433325 . A . . . GT:DP:GQ:MIN_DP:PL ./.:28:0:28:0,0,874 ./.:33:24:33:0,24,1136 -20 10433326 . A T, . . AS_RAW_BaseQRankSum=|0.8,1|;AS_RAW_MQ=12736.00|48881.00|0.00;AS_RAW_MQRankSum=|0.5,1|;AS_RAW_ReadPosRankSum=|1.4,1|;AS_SB_TABLE=2,7|13,13|0,0;BaseQRankSum=1.54;DP=67;ExcessHet=3.01;MQRankSum=0.871;RAW_MQ=118528.00;ReadPosRankSum=1.74 GT:AD:GQ:PGT:PID:PL:SB ./.:8,6,0:99:0|1:10433324_A_T:228,0,275,252,293,546:2,6,2,4 ./.:1,20,0:53:0|1:10433324_A_T:877,53,0,881,61,888:0,1,11,9 +20 10433326 . A T, . . AS_RAW_BaseQRankSum=|0.8,1|;AS_RAW_MQ=12736.00|48881.00|0.00;AS_RAW_MQRankSum=|0.5,1|;AS_RAW_ReadPosRankSum=|1.4,1|;AS_SB_TABLE=2,7|13,13|0,0;BaseQRankSum=1.54;DP=67;ExcessHet=3.01;MQRankSum=0.871;RAW_MQ=65218.00;ReadPosRankSum=1.74 GT:AD:GQ:PGT:PID:PL:SB ./.:8,6,0:99:0|1:10433324_A_T:228,0,275,252,293,546:2,6,2,4 ./.:1,20,0:53:0|1:10433324_A_T:877,53,0,881,61,888:0,1,11,9 20 10433327 . A . . . GT:DP:GQ:MIN_DP:PL ./.:27:0:27:0,0,836 ./.:32:23:32:0,23,1108 -20 10433328 . A T,AATATAT,AATATATAT,AATATATATAT,ATATAT,ATATATAT, . . AS_RAW_BaseQRankSum=|||||||;AS_RAW_MQ=0.00|48881.00|0.00|0.00|0.00|2523.00|0.00|0.00;AS_RAW_MQRankSum=|||||||;AS_RAW_ReadPosRankSum=|||||||;AS_SB_TABLE=0,0|13,13|0,0|0,0|0,0|1,2|0,0|0,0;DP=66;ExcessHet=3.01;RAW_MQ=114928.00 GT:AD:GQ:PL:SB ./.:0,6,0,0,0,3,0,0:91:919,177,246,470,91,592,513,192,470,640,676,211,616,658,804,420,0,514,384,530,500,483,122,428,576,595,379,563,676,211,616,658,804,530,595,804:0,0,3,6 ./.:0,20,0,0,0,0,0,0:74:1191,74,0,1085,90,1328,951,76,1182,1193,1147,93,1334,1214,1394,1132,93,1334,1213,1381,1376,1132,93,1334,1213,1381,1376,1376,1132,93,1334,1213,1381,1376,1376,1376:0,0,11,9 +20 10433328 . A T,ATATAT,AATATAT,ATATATAT,AATATATAT,AATATATATAT, . . AS_RAW_BaseQRankSum=|||||||;AS_RAW_MQ=0.00|48881.00|2523.00|0.00|0.00|0.00|0.00|0.00;AS_RAW_MQRankSum=|||||||;AS_RAW_ReadPosRankSum=|||||||;AS_SB_TABLE=0,0|13,13|1,2|0,0|0,0|0,0|0,0|0,0;DP=66;ExcessHet=3.01;RAW_MQ=65218.00 GT:AD:GQ:PL:SB ./.:0,6,3,0,0,0,0,0:91:919,177,246,420,0,500,470,91,514,592,483,122,379,428,563,513,192,384,470,576,640,676,211,530,616,595,658,804,676,211,530,616,595,658,804,804:0,0,3,6 ./.:0,20,0,0,0,0,0,0:74:1191,74,0,1132,93,1376,1085,90,1334,1328,1132,93,1376,1334,1376,951,76,1213,1182,1213,1193,1147,93,1381,1334,1381,1214,1394,1132,93,1376,1334,1376,1213,1381,1376:0,0,11,9 20 10433329 . A . . . GT:DP:GQ:MIN_DP:PL ./.:27:0:27:0,0,759 ./.:32:23:32:0,23,1107 20 10433330 . T . . . GT:DP:GQ:MIN_DP:PL ./.:27:12:27:0,12,900 ./.:32:61:31:0,61,1035 20 10433331 . A . . . GT:DP:GQ:MIN_DP:PL ./.:26:47:26:0,47,959 ./.:32:61:31:0,61,1035 @@ -378,7 +474,7 @@ 20 10436224 . G . . . GT:DP:GQ:MIN_DP:PL ./.:68:99:58:0,120,1800 ./.:37:37:37:0,37,1254 20 10436225 . T . . . GT:DP:GQ:MIN_DP:PL ./.:68:99:58:0,120,1800 ./.:35:66:35:0,66,990 20 10436226 . C . . . GT:DP:GQ:MIN_DP:PL ./.:68:99:58:0,120,1800 ./.:35:27:35:0,27,1218 -20 10436227 . TTTTATTTATTTATTTATTTA TTTTATTTATTTATTTATTTATTTA,T, . . AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=3600.00|48876.00|25702.00|0.00;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=1,0|11,6|14,10|0,0;BaseQRankSum=-1.450e+00;DP=108;ExcessHet=3.01;MQRankSum=-1.660e+00;RAW_MQ=313019.00;ReadPosRankSum=1.30 GT:AD:GQ:PL:SB ./.:1,7,24,0:99:1225,947,970,241,0,589,1258,1017,491,1480:1,0,18,13 ./.:0,10,0,0:29:425,29,0,427,30,428,427,30,428,428:0,0,7,3 +20 10436227 . TTTTATTTATTTATTTATTTA TTTTATTTATTTATTTATTTATTTA,T, . . AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=3600.00|48876.00|25702.00|0.00;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=1,0|11,6|14,10|0,0;BaseQRankSum=-1.450e+00;DP=108;ExcessHet=3.01;MQRankSum=-1.660e+00;RAW_MQ=201025.00;ReadPosRankSum=1.30 GT:AD:GQ:PL:SB ./.:1,7,24,0:99:1225,947,970,241,0,589,1258,1017,491,1480:1,0,18,13 ./.:0,10,0,0:29:425,29,0,427,30,428,427,30,428,428:0,0,7,3 20 10436228 . T *, . . DP=108 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:1,24,0:.:99:.:1225,241,589,1258,491,1480:1,0,18,13 ./.:.:33:0:33:0,0,688,0,688,688 20 10436229 . T *, . . DP=108 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:1,24,0:.:99:.:1225,241,589,1258,491,1480:1,0,18,13 ./.:.:33:30:33:0,30,450,30,450,450 20 10436230 . T *, . . DP=106 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:1,24,0:.:99:.:1225,241,589,1258,491,1480:1,0,18,13 ./.:.:32:33:31:0,33,495,33,495,495 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotations.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotations.vcf.idx index cea6fd665b3..8acaf8fcb1b 100644 Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotations.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotations.vcf.idx differ diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotationsNoGroup.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotationsNoGroup.vcf index 8969ee6175b..0d34fbd19ab 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotationsNoGroup.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotationsNoGroup.vcf @@ -10,8 +10,8 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine.CombineGVCFs= ##GATKCommandLine.HaplotypeCaller= +##GATKCommandLine= ##GVCFBlock0-1=minGQ=0(inclusive),maxGQ=1(exclusive) ##GVCFBlock1-2=minGQ=1(inclusive),maxGQ=2(exclusive) ##GVCFBlock10-11=minGQ=10(inclusive),maxGQ=11(exclusive) @@ -77,31 +77,127 @@ ##GVCFBlock9-10=minGQ=9(inclusive),maxGQ=10(exclusive) ##GVCFBlock90-99=minGQ=90(inclusive),maxGQ=99(exclusive) ##GVCFBlock99-100=minGQ=99(inclusive),maxGQ=100(exclusive) +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= ##INFO= -##INFO= +##INFO= +##INFO= +##INFO= ##INFO= ##INFO= ##INFO= ##INFO= +##INFO= ##INFO= +##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= +##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= +##INFO= ##INFO= ##INFO= -##contig= -##contig= -##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +##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= +##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta +##source=CombineGVCFs #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA12892 -20 10087820 . CAG CAGAGAG,CAGAGAGAG,C,CAGAG, . . AS_RAW_BaseQRankSum=||1.0,1||-2.1,1|;AS_RAW_MQ=220977.00|4441.00|47258.00|3600.00|46800.00|0.00;AS_RAW_MQRankSum=||-3.1,1||0.6,1|;AS_RAW_ReadPosRankSum=||-0.3,1||-0.4,1|;AS_SB_TABLE=33,31|0,2|12,12|1,0|8,5|0,0;BaseQRankSum=0.955;DP=167;ExcessHet=3.01;MQRankSum=0.678;RAW_MQ=541599.00;ReadPosRankSum=-2.540e-01 GT:AD:GQ:PL:SB ./.:35,0,0,1,13,0:99:302,483,1922,483,1922,1922,490,1995,1995,2306,0,1169,1169,1170,1079,483,1922,1922,1995,1169,1922:17,18,9,5 ./.:29,2,24,0,0,0:99:606,627,1620,0,864,849,697,1597,927,1653,697,1597,927,1653,1653,697,1597,927,1653,1653,1653:16,13,12,14 +20 10087820 . CAG CAGAGAG,CAGAGAGAG,C,CAGAG, . . AS_RAW_BaseQRankSum=||1.0,1||-2.1,1|;AS_RAW_MQ=220977.00|4441.00|47258.00|3600.00|46800.00|0.00;AS_RAW_MQRankSum=||-3.1,1||0.6,1|;AS_RAW_ReadPosRankSum=||-0.3,1||-0.4,1|;AS_SB_TABLE=33,31|0,2|12,12|1,0|8,5|0,0;BaseQRankSum=0.955;DP=167;ExcessHet=3.01;MQRankSum=0.678;RAW_MQ=329810.00;ReadPosRankSum=-2.540e-01 GT:AD:GQ:PL:SB ./.:35,0,0,1,13,0:99:302,483,1922,483,1922,1922,490,1995,1995,2306,0,1169,1169,1170,1079,483,1922,1922,1995,1169,1922:17,18,9,5 ./.:29,2,24,0,0,0:99:606,627,1620,0,864,849,697,1597,927,1653,697,1597,927,1653,1653,697,1597,927,1653,1653,1653:16,13,12,14 20 10087821 . A *, . . DP=93 GT:AD:GQ:PL:SB ./.:35,1,0:99:302,490,2306,483,1995,1922:17,18,9,5 ./. 20 10087822 . G *, . . DP=93 GT:AD:GQ:PL:SB ./.:35,1,0:99:302,490,2306,483,1995,1922:17,18,9,5 ./. 20 10433000 . G . . END=10433048 GT:DP:GQ:MIN_DP:PL ./.:73:99:40:0,99,1485 ./.:50:99:43:0,102,1530 @@ -198,7 +294,7 @@ 20 10433308 . G . . . GT:DP:GQ:MIN_DP:PL ./.:27:18:27:0,18,270 ./.:34:21:34:0,21,315 20 10433309 . T . . . GT:DP:GQ:MIN_DP:PL ./.:27:12:27:0,12,180 ./.:35:6:35:0,6,90 20 10433310 . C . . END=10433311 GT:DP:GQ:MIN_DP:PL ./.:27:6:27:0,6,90 ./.:35:6:35:0,6,90 -20 10433312 . CAAAAAAA C,CAAAAAA, . . AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=76598.00|0.00|1682.00|0.00;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=19,20|0,0|1,1|0,0;BaseQRankSum=1.59;DP=80;ExcessHet=3.01;MQRankSum=-1.259e+00;RAW_MQ=179123.00;ReadPosRankSum=0.333 GT:AD:GQ:PL:SB ./.:16,0,0,0:48:0,74,1123,48,615,553,75,891,606,839:6,10,0,0 ./.:23,0,2,0:10:0,81,1139,10,811,747,81,1026,798,979:13,10,1,1 +20 10433312 . CAAAAAAA C,CAAAAAA, . . AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=76598.00|0.00|1682.00|0.00;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=19,20|0,0|1,1|0,0;BaseQRankSum=1.59;DP=80;ExcessHet=3.01;MQRankSum=-1.259e+00;RAW_MQ=95936.00;ReadPosRankSum=0.333 GT:AD:GQ:PL:SB ./.:16,0,0,0:48:0,74,1123,48,615,553,75,891,606,839:6,10,0,0 ./.:23,0,2,0:10:0,81,1139,10,811,747,81,1026,798,979:13,10,1,1 20 10433313 . A *, . . DP=80 GT:AD:GQ:PL:SB ./.:16,0,0:48:0,48,553,75,606,839:6,10,0,0 ./.:23,2,0:10:0,10,747,81,798,979:13,10,1,1 20 10433314 . A *, . . DP=80 GT:AD:GQ:PL:SB ./.:16,0,0:48:0,48,553,75,606,839:6,10,0,0 ./.:23,2,0:10:0,10,747,81,798,979:13,10,1,1 20 10433315 . A *, . . DP=80 GT:AD:GQ:PL:SB ./.:16,0,0:48:0,48,553,75,606,839:6,10,0,0 ./.:23,2,0:10:0,10,747,81,798,979:13,10,1,1 @@ -208,13 +304,13 @@ 20 10433319 . A *, . . DP=80 GT:AD:GQ:PL:SB ./.:16,0,0:48:0,48,553,75,606,839:6,10,0,0 ./.:23,2,0:10:0,10,747,81,798,979:13,10,1,1 20 10433320 . A . . . GT:DP:GQ:MIN_DP:PL ./.:25:0:25:0,0,708 ./.:34:0:34:0,0,1030 20 10433321 . A . . . GT:DP:GQ:MIN_DP:PL ./.:29:33:29:0,33,495 ./.:35:21:35:0,21,315 -20 10433322 . A AT,ATAT, . . AS_RAW_BaseQRankSum=|0.8,1,2.5,1||;AS_RAW_MQ=17782.00|41312.00|2523.00|0.00;AS_RAW_MQRankSum=|1.1,1,2.2,1||;AS_RAW_ReadPosRankSum=|1.9,1,2.0,1||;AS_SB_TABLE=7,8|8,9|2,1|0,0;BaseQRankSum=2.56;DP=77;ExcessHet=3.01;MQRankSum=1.90;RAW_MQ=154528.00;ReadPosRankSum=2.04 GT:AD:GQ:PL:SB ./.:11,5,0,0:99:124,0,369,158,384,542,158,384,542,542:5,6,2,3 ./.:4,12,3,0:19:450,0,46,298,19,576,442,117,506,617:2,2,8,7 +20 10433322 . A AT,ATAT, . . AS_RAW_BaseQRankSum=|0.8,1,2.5,1||;AS_RAW_MQ=17782.00|41312.00|2523.00|0.00;AS_RAW_MQRankSum=|1.1,1,2.2,1||;AS_RAW_ReadPosRankSum=|1.9,1,2.0,1||;AS_SB_TABLE=7,8|8,9|2,1|0,0;BaseQRankSum=2.56;DP=77;ExcessHet=3.01;MQRankSum=1.90;RAW_MQ=86818.00;ReadPosRankSum=2.04 GT:AD:GQ:PL:SB ./.:11,5,0,0:99:124,0,369,158,384,542,158,384,542,542:5,6,2,3 ./.:4,12,3,0:19:450,0,46,298,19,576,442,117,506,617:2,2,8,7 20 10433323 . A . . . GT:DP:GQ:MIN_DP:PL ./.:29:0:29:0,0,502 ./.:34:0:34:0,0,0 -20 10433324 . A T, . . AS_RAW_BaseQRankSum=|2.2,1|;AS_RAW_MQ=12736.00|48881.00|0.00;AS_RAW_MQRankSum=|0.5,1|;AS_RAW_ReadPosRankSum=|1.5,1|;AS_SB_TABLE=2,7|13,13|0,0;BaseQRankSum=2.28;DP=73;ExcessHet=3.01;MQRankSum=0.871;RAW_MQ=140128.00;ReadPosRankSum=1.74 GT:AD:GQ:PGT:PID:PL:SB ./.:8,6,0:99:0|1:10433324_A_T:228,0,275,252,294,546:2,6,2,4 ./.:1,20,0:53:0|1:10433324_A_T:877,53,0,880,61,888:0,1,11,9 +20 10433324 . A T, . . AS_RAW_BaseQRankSum=|2.2,1|;AS_RAW_MQ=12736.00|48881.00|0.00;AS_RAW_MQRankSum=|0.5,1|;AS_RAW_ReadPosRankSum=|1.5,1|;AS_SB_TABLE=2,7|13,13|0,0;BaseQRankSum=2.28;DP=73;ExcessHet=3.01;MQRankSum=0.871;RAW_MQ=79618.00;ReadPosRankSum=1.74 GT:AD:GQ:PGT:PID:PL:SB ./.:8,6,0:99:0|1:10433324_A_T:228,0,275,252,294,546:2,6,2,4 ./.:1,20,0:53:0|1:10433324_A_T:877,53,0,880,61,888:0,1,11,9 20 10433325 . A . . . GT:DP:GQ:MIN_DP:PL ./.:28:0:28:0,0,874 ./.:33:24:33:0,24,1136 -20 10433326 . A T, . . AS_RAW_BaseQRankSum=|0.8,1|;AS_RAW_MQ=12736.00|48881.00|0.00;AS_RAW_MQRankSum=|0.5,1|;AS_RAW_ReadPosRankSum=|1.4,1|;AS_SB_TABLE=2,7|13,13|0,0;BaseQRankSum=1.54;DP=67;ExcessHet=3.01;MQRankSum=0.871;RAW_MQ=118528.00;ReadPosRankSum=1.74 GT:AD:GQ:PGT:PID:PL:SB ./.:8,6,0:99:0|1:10433324_A_T:228,0,275,252,293,546:2,6,2,4 ./.:1,20,0:53:0|1:10433324_A_T:877,53,0,881,61,888:0,1,11,9 +20 10433326 . A T, . . AS_RAW_BaseQRankSum=|0.8,1|;AS_RAW_MQ=12736.00|48881.00|0.00;AS_RAW_MQRankSum=|0.5,1|;AS_RAW_ReadPosRankSum=|1.4,1|;AS_SB_TABLE=2,7|13,13|0,0;BaseQRankSum=1.54;DP=67;ExcessHet=3.01;MQRankSum=0.871;RAW_MQ=65218.00;ReadPosRankSum=1.74 GT:AD:GQ:PGT:PID:PL:SB ./.:8,6,0:99:0|1:10433324_A_T:228,0,275,252,293,546:2,6,2,4 ./.:1,20,0:53:0|1:10433324_A_T:877,53,0,881,61,888:0,1,11,9 20 10433327 . A . . . GT:DP:GQ:MIN_DP:PL ./.:27:0:27:0,0,836 ./.:32:23:32:0,23,1108 -20 10433328 . A T,AATATAT,AATATATAT,AATATATATAT,ATATAT,ATATATAT, . . AS_RAW_BaseQRankSum=|||||||;AS_RAW_MQ=0.00|48881.00|0.00|0.00|0.00|2523.00|0.00|0.00;AS_RAW_MQRankSum=|||||||;AS_RAW_ReadPosRankSum=|||||||;AS_SB_TABLE=0,0|13,13|0,0|0,0|0,0|1,2|0,0|0,0;DP=66;ExcessHet=3.01;RAW_MQ=114928.00 GT:AD:GQ:PL:SB ./.:0,6,0,0,0,3,0,0:91:919,177,246,470,91,592,513,192,470,640,676,211,616,658,804,420,0,514,384,530,500,483,122,428,576,595,379,563,676,211,616,658,804,530,595,804:0,0,3,6 ./.:0,20,0,0,0,0,0,0:74:1191,74,0,1085,90,1328,951,76,1182,1193,1147,93,1334,1214,1394,1132,93,1334,1213,1381,1376,1132,93,1334,1213,1381,1376,1376,1132,93,1334,1213,1381,1376,1376,1376:0,0,11,9 +20 10433328 . A T,ATATAT,AATATAT,ATATATAT,AATATATAT,AATATATATAT, . . AS_RAW_BaseQRankSum=|||||||;AS_RAW_MQ=0.00|48881.00|2523.00|0.00|0.00|0.00|0.00|0.00;AS_RAW_MQRankSum=|||||||;AS_RAW_ReadPosRankSum=|||||||;AS_SB_TABLE=0,0|13,13|1,2|0,0|0,0|0,0|0,0|0,0;DP=66;ExcessHet=3.01;RAW_MQ=65218.00 GT:AD:GQ:PL:SB ./.:0,6,3,0,0,0,0,0:91:919,177,246,420,0,500,470,91,514,592,483,122,379,428,563,513,192,384,470,576,640,676,211,530,616,595,658,804,676,211,530,616,595,658,804,804:0,0,3,6 ./.:0,20,0,0,0,0,0,0:74:1191,74,0,1132,93,1376,1085,90,1334,1328,1132,93,1376,1334,1376,951,76,1213,1182,1213,1193,1147,93,1381,1334,1381,1214,1394,1132,93,1376,1334,1376,1213,1381,1376:0,0,11,9 20 10433329 . A . . . GT:DP:GQ:MIN_DP:PL ./.:27:0:27:0,0,759 ./.:32:23:32:0,23,1107 20 10433330 . T . . . GT:DP:GQ:MIN_DP:PL ./.:27:12:27:0,12,900 ./.:32:61:31:0,61,1035 20 10433331 . A . . . GT:DP:GQ:MIN_DP:PL ./.:26:47:26:0,47,959 ./.:32:61:31:0,61,1035 @@ -378,7 +474,7 @@ 20 10436224 . G . . . GT:DP:GQ:MIN_DP:PL ./.:68:99:58:0,120,1800 ./.:37:37:37:0,37,1254 20 10436225 . T . . . GT:DP:GQ:MIN_DP:PL ./.:68:99:58:0,120,1800 ./.:35:66:35:0,66,990 20 10436226 . C . . . GT:DP:GQ:MIN_DP:PL ./.:68:99:58:0,120,1800 ./.:35:27:35:0,27,1218 -20 10436227 . TTTTATTTATTTATTTATTTA TTTTATTTATTTATTTATTTATTTA,T, . . AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=3600.00|48876.00|25702.00|0.00;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=1,0|11,6|14,10|0,0;BaseQRankSum=-1.450e+00;DP=108;ExcessHet=3.01;MQRankSum=-1.660e+00;RAW_MQ=313019.00;ReadPosRankSum=1.30 GT:AD:GQ:PL:SB ./.:1,7,24,0:99:1225,947,970,241,0,589,1258,1017,491,1480:1,0,18,13 ./.:0,10,0,0:29:425,29,0,427,30,428,427,30,428,428:0,0,7,3 +20 10436227 . TTTTATTTATTTATTTATTTA TTTTATTTATTTATTTATTTATTTA,T, . . AS_RAW_BaseQRankSum=|||;AS_RAW_MQ=3600.00|48876.00|25702.00|0.00;AS_RAW_MQRankSum=|||;AS_RAW_ReadPosRankSum=|||;AS_SB_TABLE=1,0|11,6|14,10|0,0;BaseQRankSum=-1.450e+00;DP=108;ExcessHet=3.01;MQRankSum=-1.660e+00;RAW_MQ=201025.00;ReadPosRankSum=1.30 GT:AD:GQ:PL:SB ./.:1,7,24,0:99:1225,947,970,241,0,589,1258,1017,491,1480:1,0,18,13 ./.:0,10,0,0:29:425,29,0,427,30,428,427,30,428,428:0,0,7,3 20 10436228 . T *, . . DP=108 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:1,24,0:.:99:.:1225,241,589,1258,491,1480:1,0,18,13 ./.:.:33:0:33:0,0,688,0,688,688 20 10436229 . T *, . . DP=108 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:1,24,0:.:99:.:1225,241,589,1258,491,1480:1,0,18,13 ./.:.:33:30:33:0,30,450,30,450,450 20 10436230 . T *, . . DP=106 GT:AD:DP:GQ:MIN_DP:PL:SB ./.:1,24,0:.:99:.:1225,241,589,1258,491,1480:1,0,18,13 ./.:.:32:33:31:0,33,495,33,495,495 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotationsNoGroup.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotationsNoGroup.vcf.idx index 30e731fc9a2..321c1800686 100644 Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotationsNoGroup.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testAlleleSpecificAnnotationsNoGroup.vcf.idx differ diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBasepairResolutionInput.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBasepairResolutionInput.vcf index 44de9b48eb2..63b01a39ce5 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBasepairResolutionInput.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBasepairResolutionInput.vcf @@ -7,11 +7,16 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine.CombineGVCFs= +##GATKCommandLine= +##INFO= +##INFO= +##INFO= ##INFO= ##INFO= ##INFO= ##INFO= +##INFO= +##INFO= ##INFO= ##INFO= ##INFO= @@ -19,10 +24,95 @@ ##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= -##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +##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/1kg/reference/human_g1k_v37.fasta +##source=CombineGVCFs #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 20 10000000 . T . . . GT:AD:DP:GQ:PL ./.:52,0:52:99:0,120,1800 20 10000001 . T . . . GT:AD:DP:GQ:PL ./.:54,0:54:99:0,120,1800 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBasepairResolutionInput.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBasepairResolutionInput.vcf.idx index 51dddd03dba..2c216f9871c 100644 Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBasepairResolutionInput.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBasepairResolutionInput.vcf.idx differ diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBreakBandsArgumet.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBreakBandsArgumet.vcf index e03a2250ffa..503ed36f69a 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBreakBandsArgumet.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBreakBandsArgumet.vcf @@ -8,20 +8,114 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine.CombineGVCFs= +##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) +##INFO= +##INFO= +##INFO= ##INFO= ##INFO= +##INFO= ##INFO= ##INFO= +##INFO= +##INFO= ##INFO= +##INFO= ##INFO= ##INFO= ##INFO= +##INFO= ##INFO= -##contig= -##contig= -##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +##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:///Users/ebanks/Sting_unstable/../references/hs37d5.fasta +##source=CombineGVCFs ##source=SelectVariants #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA1 NA2 20 69491 . G . . END=69494 GT:DP:GQ:MIN_DP:MIN_GQ:PL ./.:94:99:82:99:0,120,1800 ./. diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBreakBandsArgumet.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBreakBandsArgumet.vcf.idx index 449c4687095..6b3586b521c 100644 Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBreakBandsArgumet.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testBreakBandsArgumet.vcf.idx differ diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf index eb181008ce8..fed91083631 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf @@ -8,13 +8,24 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine.CombineGVCFs= +##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) +##INFO= +##INFO= +##INFO= +##INFO= ##INFO= ##INFO= -##contig= -##contig= -##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##contig= +##source=CombineGVCFs #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA1 20 3944040 . A . . END=3944042 GT:DP:GQ:MIN_DP:PL ./.:81:60:76:0,60,900 20 3944043 . ATTT A,AT,ATT, . . DP=63 GT:AD:DP:GQ:PL:SB ./.:7,4,16,36,0:63:99:1169,1026,1642,629,917,839,278,269,0,257,1020,1140,771,337,1103:5,2,49,7 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf.idx index 913ed4065f4..f92a73f1d2b 100644 Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSample.vcf.idx differ diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleHaploid.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleHaploid.vcf index 3052b6e599a..5e8f1b07fc7 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleHaploid.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleHaploid.vcf @@ -8,13 +8,24 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine.CombineGVCFs= +##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) +##INFO= +##INFO= +##INFO= +##INFO= ##INFO= ##INFO= -##contig= -##contig= -##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##contig= +##source=CombineGVCFs #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA1 20 3944040 . A . . END=3944042 GT:DP:GQ:MIN_DP:PL .:81:60:76:0,900 20 3944043 . ATTT A,AT,ATT, . . DP=63 GT:AD:DP:GQ:PL:SB .:7,4,16,36,0:63:99:1169,839,0,257,999:5,2,49,7 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleHaploid.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleHaploid.vcf.idx index 45484960759..1c01a4a4c6a 100644 Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleHaploid.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleHaploid.vcf.idx differ diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf index a19a8136860..8829a8bae5c 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf @@ -8,13 +8,24 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine.CombineGVCFs= +##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=5(exclusive) +##INFO= +##INFO= +##INFO= +##INFO= ##INFO= ##INFO= -##contig= -##contig= -##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##contig= +##source=CombineGVCFs #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA1 20 3944040 . A . . END=3944042 GT:DP:GQ:MIN_DP:PL ./././.:81:60:76:0,60,100,300,900 20 3944043 . ATTT A,AT, . . DP=63 GT:AD:DP:GQ:PL:SB ./././.:7,4,16,36:63:99:600,501,502,503,800,505,506,507,508,509,510,511,512,513,700,515,516,517,518,519,520,521,522,523,524,525,526,527,528,529,530,531,532,533,900:5,2,49,7 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf.idx index 354963f82e5..b076169db5c 100644 Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testMultipleSpanningDeletionsForOneSampleTetraploid.vcf.idx differ diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testWrongReferenceBaseBugFix.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testWrongReferenceBaseBugFix.vcf index d33c13d0be5..136b0578291 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testWrongReferenceBaseBugFix.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testWrongReferenceBaseBugFix.vcf @@ -10,14 +10,19 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine.CombineGVCFs= +##GATKCommandLine= ##GVCFBlock=minGQ=0(inclusive),maxGQ=1(exclusive) +##INFO= +##INFO= +##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= +##INFO= +##INFO= ##INFO= ##INFO= ##INFO= @@ -25,10 +30,95 @@ ##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= -##reference=file:///Users/emeryj/hellbender/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta +##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://human_g1k_v37.fasta +##source=CombineGVCFs #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ind3 ind4 20 762273 rs3115849 G A, . . DP=311;MQ=41.16;MQ0=0 GT:AD:DP:GQ:PL:SB ./.:0,152,0:152:99:5359,457,0,5359,457,5359:0,0,11,141 ./.:0,157,0:157:99:5441,472,0,5441,472,5441:0,0,15,142 20 762274 . G . . END=762302 GT:DP:GQ:MIN_DP:PL ./.:113:99:102:0,120,1800 ./.:88:99:46:0,99,1485 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testWrongReferenceBaseBugFix.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testWrongReferenceBaseBugFix.vcf.idx index 65c6696f7e6..6ac93fab572 100644 Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testWrongReferenceBaseBugFix.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/testWrongReferenceBaseBugFix.vcf.idx differ diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf index f0b26576f10..67be150150a 100644 --- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf +++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf @@ -12,8 +12,8 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##GATKCommandLine= -##GATKCommandLine= +##GATKCommandLine= +##GATKCommandLine= ##GATKCommandLine= ##INFO= ##INFO= @@ -188,8 +188,8 @@ 20 10008742 . G T 1276.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=3.89;ClippingRankSum=0.00;DP=84;ExcessHet=4.7712;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=47.37;MQRankSum=-1.113e+00;QD=15.57;ReadPosRankSum=0.221;SOR=0.757 GT:AD:DP:GQ:PL 0/1:23,26:49:99:744,0,580 0/1:13,20:33:99:542,0,265 20 10008758 . C CA,CAA 1502.15 . AC=3,1;AF=0.750,0.250;AN=4;BaseQRankSum=0.130;DP=81;ExcessHet=3.0103;FS=2.124;MLEAC=3,1;MLEAF=0.750,0.250;MQ=47.46;MQRankSum=-1.168e+00;QD=22.76;ReadPosRankSum=-5.200e-02;SOR=0.324 GT:AD:DP:GQ:PL 1/1:4,31,0:35:10:721,10,0,733,102,825 1/2:0,20,11:31:99:804,284,194,434,0,396 20 10008921 . C CA 283.27 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.610;DP=80;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=56.34;MQRankSum=-1.906e+00;QD=8.33;ReadPosRankSum=0.173;SOR=0.512 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:18,16:34:99:0|1:10008921_C_CA:291,0,366:10008921 0/0:31,0:31:6:.:.:0,6,658 -20 10008948 . TA T 3485.09 . AC=4;AF=1.00;AN=4;BaseQRankSum=0.994;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=54.92;MQRankSum=2.05;QD=33.27;ReadPosRankSum=0.884;SOR=0.446 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:1,50:51:99:1|1:10008921_C_CA:2095,107,0:10008921 1/1:0,33:33:99:.:.:1406,99,0 -20 10008952 . CACACACACACA C,CCACACACA,CCACACACACA,CCA 2985.19 . AC=1,1,1,1;AF=0.250,0.250,0.250,0.250;AN=4;BaseQRankSum=0.941;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=1,1,1,1;MLEAF=0.250,0.250,0.250,0.250;MQ=54.55;MQRankSum=1.84;QD=31.26;ReadPosRankSum=0.716;SOR=0.487 GT:AD:DP:GQ:PL 1/3:1,14,5,11,0:34:99:1704,525,845,726,173,703,582,0,443,530,1135,744,779,607,1321 2/4:0,0,15,0,12:27:99:1315,1243,1282,505,512,439,1243,1282,512,1282,648,714,0,714,719 +20 10008948 . TA T 3495.09 . AC=4;AF=1.00;AN=4;BaseQRankSum=0.994;DP=85;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=54.92;MQRankSum=2.05;QD=33.27;ReadPosRankSum=0.884;SOR=0.446 GT:AD:DP:GQ:PGT:PID:PL:PS 1|1:1,50:51:99:1|1:10008921_C_CA:2105,117,0:10008921 1/1:0,33:33:99:.:.:1406,99,0 +20 10008952 . CACACACACACA C,CCACACACA,CCACACACACA,CCA 2998.19 . AC=1,1,1,1;AF=0.250,0.250,0.250,0.250;AN=4;BaseQRankSum=0.941;DP=95;ExcessHet=3.0103;FS=0.000;MLEAC=1,1,1,1;MLEAF=0.250,0.250,0.250,0.250;MQ=54.55;MQRankSum=1.84;QD=31.26;ReadPosRankSum=0.716;SOR=0.487 GT:AD:DP:GQ:PL 1/3:1,14,5,11,0:34:99:1717,539,803,739,154,687,596,0,443,533,1149,712,761,607,1292 2/4:0,0,15,0,12:27:99:1315,1243,1282,505,512,439,1243,1282,512,1282,648,714,0,714,719 20 10009227 . A G 2028.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=-1.130e-01;ClippingRankSum=0.00;DP=103;ExcessHet=4.7712;FS=1.650;MLEAC=2;MLEAF=0.500;MQ=58.31;MQRankSum=1.43;QD=19.89;ReadPosRankSum=-1.119e+00;SOR=0.502 GT:AD:DP:GQ:PGT:PID:PL:PS 0/1:23,39:62:99:.:.:1398,0,740 0/1:16,24:40:99:0|1:10009227_A_G:640,0,377:10009227 20 10009246 . A G 4327.09 . AC=4;AF=1.00;AN=4;BaseQRankSum=1.56;ClippingRankSum=0.00;DP=114;ExcessHet=3.0103;FS=3.371;MLEAC=4;MLEAF=1.00;MQ=57.39;MQRankSum=0.00;QD=27.76;ReadPosRankSum=1.72;SOR=0.514 GT:AD:DP:GQ:PGT:PID:PL:PS 1/1:0,77:77:99:.:.:3031,231,0 1/1:1,35:36:99:1|1:10009227_A_G:1312,101,0:10009227 20 10009400 . T A 4867.09 . AC=4;AF=1.00;AN=4;DP=132;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=60.00;QD=29.09;SOR=0.820 GT:AD:DP:GQ:PL 1/1:0,74:74:99:3027,223,0 1/1:0,58:58:99:1856,174,0 @@ -253,9 +253,9 @@ 20 10024951 . G T 941.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=1.14;ClippingRankSum=0.00;DP=80;ExcessHet=3.0103;FS=7.110;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=22.97;ReadPosRankSum=-8.000e-02;SOR=1.770 GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:39,0:39:99:.:.:0,105,1509 0/1:17,24:41:99:0|1:10024950_G_T:950,0,913:10024950 20 10026357 . T C 1679.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=-6.420e-01;ClippingRankSum=0.00;DP=102;ExcessHet=4.7712;FS=11.376;MLEAC=2;MLEAF=0.500;MQ=59.04;MQRankSum=0.00;QD=16.63;ReadPosRankSum=1.62;SOR=0.779 GT:AD:DP:GQ:PL 0/1:28,35:63:99:1195,0,932 0/1:19,19:38:99:494,0,521 20 10026794 . C T 1704.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=2.83;ClippingRankSum=0.00;DP=104;ExcessHet=4.7712;FS=0.732;MLEAC=2;MLEAF=0.500;MQ=59.78;MQRankSum=0.00;QD=16.55;ReadPosRankSum=-5.330e-01;SOR=0.783 GT:AD:DP:GQ:PL 0/1:19,33:52:99:1113,0,529 0/1:27,24:51:99:601,0,657 -20 10027234 . A ATTAG 3111.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-4.060e-01;ClippingRankSum=0.00;DP=113;ExcessHet=3.0103;FS=1.661;MLEAC=3;MLEAF=0.750;MQ=58.61;MQRankSum=0.375;QD=28.28;ReadPosRankSum=0.211;SOR=0.849 GT:AD:DP:GQ:PL 0/1:34,35:69:99:1358,0,1964 1/1:1,40:41:65:1767,65,0 -20 10027868 . A G 2685.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=-4.141e+00;ClippingRankSum=0.00;DP=134;ExcessHet=4.7712;FS=6.535;MLEAC=2;MLEAF=0.500;MQ=59.66;MQRankSum=0.032;QD=20.34;ReadPosRankSum=1.87;SOR=0.956 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:44,45:89:99:0|1:10027868_A_G:1768,0,3201:10027868 0/1:19,24:43:99:0|1:10027868_A_G:927,0,1091:10027868 -20 10027872 . A G 2670.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=-8.550e-01;ClippingRankSum=0.00;DP=129;ExcessHet=4.7712;FS=9.561;MLEAC=2;MLEAF=0.500;MQ=59.64;MQRankSum=0.101;QD=21.03;ReadPosRankSum=1.05;SOR=0.897 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:40,45:85:99:0|1:10027868_A_G:1753,0,3136:10027868 0/1:18,24:42:99:0|1:10027868_A_G:927,0,1091:10027868 +20 10027234 . A ATTAG 3111.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-4.060e-01;ClippingRankSum=0.00;DP=113;ExcessHet=3.0103;FS=1.661;MLEAC=3;MLEAF=0.750;MQ=58.61;MQRankSum=0.375;QD=28.28;ReadPosRankSum=0.211;SOR=0.849 GT:AD:DP:GQ:PL 0/1:34,35:69:99:1358,0,1320 1/1:1,40:41:65:1767,65,0 +20 10027868 . A G 2685.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=-4.141e+00;ClippingRankSum=0.00;DP=134;ExcessHet=4.7712;FS=6.535;MLEAC=2;MLEAF=0.500;MQ=59.66;MQRankSum=0.032;QD=20.34;ReadPosRankSum=1.87;SOR=0.956 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:44,45:89:99:0|1:10027868_A_G:1768,0,1671:10027868 0/1:19,24:43:99:0|1:10027868_A_G:927,0,1091:10027868 +20 10027872 . A G 2670.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=-8.550e-01;ClippingRankSum=0.00;DP=129;ExcessHet=4.7712;FS=9.561;MLEAC=2;MLEAF=0.500;MQ=59.64;MQRankSum=0.101;QD=21.03;ReadPosRankSum=1.05;SOR=0.897 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:40,45:85:99:0|1:10027868_A_G:1753,0,1606:10027868 0/1:18,24:42:99:0|1:10027868_A_G:927,0,1091:10027868 20 10028302 . G T 625.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=1.50;ClippingRankSum=0.00;DP=104;ExcessHet=3.0103;FS=13.880;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=13.04;ReadPosRankSum=0.800;SOR=2.280 GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:55,0:55:99:.:.:0,120,1800 0/1:30,18:48:99:0|1:10028302_G_T:634,0,1476:10028302 20 10028316 . C T 612.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.911;ClippingRankSum=0.00;DP=98;ExcessHet=3.0103;FS=6.822;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=14.59;ReadPosRankSum=-7.190e-01;SOR=1.715 GT:AD:DP:GQ:PGT:PID:PL:PS 0/0:55,0:55:99:.:.:0,120,1800 0/1:25,17:42:99:0|1:10028302_G_T:621,0,1379:10028302 20 10028725 . A G 458.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=-2.165e+00;ClippingRankSum=0.00;DP=91;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=12.75;ReadPosRankSum=0.184;SOR=0.892 GT:AD:DP:GQ:PL 0/0:55,0:55:99:0,120,1800 0/1:17,19:36:99:467,0,436 @@ -271,10 +271,10 @@ 20 10032094 . G A 1916.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=5.49;ClippingRankSum=0.00;DP=132;ExcessHet=4.7712;FS=9.336;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=14.63;ReadPosRankSum=0.092;SOR=0.468 GT:AD:DP:GQ:PL 0/1:47,36:83:99:1249,0,1497 0/1:21,27:48:99:677,0,458 20 10032413 . T G 1453.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=-2.742e+00;ClippingRankSum=0.00;DP=116;ExcessHet=4.7712;FS=8.785;MLEAC=2;MLEAF=0.500;MQ=59.68;MQRankSum=0.00;QD=12.64;ReadPosRankSum=-1.110e-01;SOR=1.453 GT:AD:DP:GQ:PL 0/1:35,31:66:99:898,0,1277 0/1:23,26:49:99:565,0,554 20 10032882 . A T 2523.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.280e-01;ClippingRankSum=0.00;DP=119;ExcessHet=3.0103;FS=9.634;MLEAC=3;MLEAF=0.750;MQ=59.81;MQRankSum=0.00;QD=21.56;ReadPosRankSum=0.626;SOR=0.225 GT:AD:DP:GQ:PL 0/1:39,36:75:99:1231,0,1406 1/1:1,41:42:93:1306,93,0 -20 10032972 . C CAT 3090.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-3.540e-01;DP=109;ExcessHet=3.0103;FS=2.753;MLEAC=3;MLEAF=0.750;MQ=59.89;MQRankSum=-1.017e+00;QD=29.15;ReadPosRankSum=-1.232e+00;SOR=0.921 GT:AD:DP:GQ:PL 0/1:33,30:63:99:1160,0,1477 1/1:0,43:43:99:1944,132,0 +20 10032972 . C CAT 3090.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=-3.540e-01;DP=109;ExcessHet=3.0103;FS=2.753;MLEAC=3;MLEAF=0.750;MQ=59.89;MQRankSum=-1.017e+00;QD=29.15;ReadPosRankSum=-1.232e+00;SOR=0.921 GT:AD:DP:GQ:PL 0/1:33,30:63:99:1160,0,1295 1/1:0,43:43:99:1944,132,0 20 10034306 . T C 1287.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=-2.200e-01;ClippingRankSum=0.00;DP=107;ExcessHet=4.7712;FS=2.552;MLEAC=2;MLEAF=0.500;MQ=59.61;MQRankSum=1.15;QD=12.26;ReadPosRankSum=0.885;SOR=1.023 GT:AD:DP:GQ:PL 0/1:46,29:75:99:811,0,1593 0/1:11,19:30:99:486,0,219 20 10034425 . C T 551.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=1.76;ClippingRankSum=0.00;DP=87;ExcessHet=3.0103;FS=5.760;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=17.25;ReadPosRankSum=-8.950e-01;SOR=0.499 GT:AD:DP:GQ:PL 0/0:55,0:55:99:0,120,1800 0/1:10,22:32:99:560,0,175 -20 10036930 . CGATAGCCCTAGCCCTAGATA C 1551.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=0.200;ClippingRankSum=0.00;DP=129;ExcessHet=4.7712;FS=10.062;MLEAC=2;MLEAF=0.500;MQ=55.99;MQRankSum=0.00;QD=15.36;ReadPosRankSum=0.460;SOR=0.213 GT:AD:DP:GQ:PL 0/1:39,29:68:99:1074,0,5571 0/1:20,13:33:99:487,0,3108 +20 10036930 . CGATAGCCCTAGCCCTAGATA C 1551.46 . AC=2;AF=0.500;AN=4;BaseQRankSum=0.200;ClippingRankSum=0.00;DP=129;ExcessHet=4.7712;FS=10.062;MLEAC=2;MLEAF=0.500;MQ=55.99;MQRankSum=0.00;QD=15.36;ReadPosRankSum=0.460;SOR=0.213 GT:AD:DP:GQ:PL 0/1:39,29:68:99:1074,0,1505 0/1:20,13:33:99:487,0,3108 20 10037037 . C T 1456.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=3.50;DP=116;ExcessHet=3.0103;FS=1.943;MLEAC=1;MLEAF=0.250;MQ=60.17;MQRankSum=-1.193e+00;QD=17.99;ReadPosRankSum=-1.609e+00;SOR=0.495 GT:AD:DP:GQ:PL 0/1:39,42:81:99:1465,0,1124 0/0:35,0:35:99:0,102,1530 20 10037110 . T TGATA 4493.13 . AC=4;AF=1.00;AN=4;DP=111;ExcessHet=3.0103;FS=0.000;MLEAC=4;MLEAF=1.00;MQ=57.85;QD=35.92;SOR=0.941 GT:AD:DP:GQ:PL 1/1:0,61:61:99:2818,189,0 1/1:0,36:36:99:1691,114,0 20 10037144 . TGATA T,TGATAGATA,TGATAGATAGATA 3048.12 . AC=1,1,2;AF=0.250,0.250,0.500;AN=4;DP=110;ExcessHet=3.0103;FS=0.000;MLEAC=1,1,2;MLEAF=0.250,0.250,0.500;MQ=54.72;QD=29.63;SOR=1.000 GT:AD:DP:GQ:PL 3/3:0,0,0,36:36:99:1861,1864,1866,1864,1866,1866,127,129,129,0 1/2:0,18,11,0:29:99:1218,461,407,756,0,724,1218,462,757,1218 @@ -291,7 +291,7 @@ 20 10042319 . C T 3236.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=1.66;ClippingRankSum=0.00;DP=108;ExcessHet=3.0103;FS=8.399;MLEAC=3;MLEAF=0.750;MQ=59.40;MQRankSum=0.00;QD=29.96;ReadPosRankSum=-8.950e-01;SOR=0.795 GT:AD:DP:GQ:PL 1/1:0,66:66:99:2687,199,0 0/1:21,21:42:99:563,0,514 20 10042761 . A G 4329.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=-2.960e-01;ClippingRankSum=0.00;DP=143;ExcessHet=3.0103;FS=0.870;MLEAC=3;MLEAF=0.750;MQ=60.00;MQRankSum=0.00;QD=30.27;ReadPosRankSum=-7.100e-02;SOR=0.863 GT:AD:DP:GQ:PL 1/1:0,91:91:99:3582,272,0 0/1:23,29:52:99:761,0,602 20 10042829 . A G 3850.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.650e-01;ClippingRankSum=0.00;DP=134;ExcessHet=3.0103;FS=0.852;MLEAC=3;MLEAF=0.750;MQ=59.86;MQRankSum=0.00;QD=28.95;ReadPosRankSum=-8.090e-01;SOR=0.556 GT:AD:DP:GQ:PL 1/1:0,78:78:99:3084,235,0 0/1:24,31:55:99:780,0,566 -20 10043002 . A T 1307.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=3.99;DP=126;ExcessHet=3.0103;FS=2.877;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=15.21;ReadPosRankSum=-3.500e-02;SOR=0.434 GT:AD:DP:GQ:PL 0/1:48,38:86:99:1316,0,1659 0/0:40,0:40:99:0,109,1146 +20 10043002 . A T 1307.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=3.99;DP=126;ExcessHet=3.0103;FS=2.877;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=15.21;ReadPosRankSum=-3.500e-02;SOR=0.434 GT:AD:DP:GQ:PL 0/1:48,38:86:99:1316,0,1658 0/0:40,0:40:99:0,109,1146 20 10044650 . A G 643.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=-5.504e+00;ClippingRankSum=0.00;DP=98;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=11.92;ReadPosRankSum=0.426;SOR=0.636 GT:AD:DP:GQ:PL 0/0:44,0:44:99:0,104,1655 0/1:24,30:54:99:652,0,625 20 10044849 . A G 2104.44 . AC=2;AF=0.500;AN=4;DP=98;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=59.61;QD=28.76;SOR=1.316 GT:AD:DP:GQ:PL 1/1:0,59:59:99:2120,177,0 0/0:39,0:39:99:0,105,1212 20 10045078 . G T 3284.44 . AC=2;AF=0.500;AN=4;DP=120;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=58.73;QD=29.94;SOR=0.876 GT:AD:DP:GQ:PL 1/1:0,81:81:99:3300,244,0 0/0:39,0:39:99:0,105,1212 @@ -406,9 +406,9 @@ 20 10088747 . A G 3164.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=-3.877e+00;DP=102;ExcessHet=3.0103;FS=7.652;MLEAC=3;MLEAF=0.750;MQ=55.74;MQRankSum=-4.907e+00;QD=31.33;ReadPosRankSum=9.000e-03;SOR=0.764 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:25,29:54:99:0|1:10088730_G_A:1140,0,995:10088730 1/1:0,47:47:99:1|1:10088730_G_A:2038,144,0:10088730 20 10088799 . G A 2353.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=5.50;DP=94;ExcessHet=3.0103;FS=8.265;MLEAC=3;MLEAF=0.750;MQ=56.15;MQRankSum=-2.498e+00;QD=25.30;ReadPosRankSum=1.08;SOR=0.604 GT:AD:DP:GQ:PL 0/1:22,31:53:99:1047,0,617 1/1:0,40:40:99:1320,120,0 20 10088895 . C T 1479.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=2.46;DP=74;ExcessHet=3.0103;FS=2.120;MLEAC=3;MLEAF=0.750;MQ=58.26;MQRankSum=0.577;QD=20.54;ReadPosRankSum=1.30;SOR=0.633 GT:AD:DP:GQ:PL 0/1:23,18:41:99:561,0,673 1/1:0,31:31:92:932,92,0 -20 10088968 . C CAAA 2980.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=0.552;DP=95;ExcessHet=3.0103;FS=1.907;MLEAC=3;MLEAF=0.750;MQ=55.48;MQRankSum=-4.750e+00;QD=31.67;ReadPosRankSum=2.42;SOR=1.012 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:30,23:53:99:0|1:10088968_C_CAAA:1213,0,1367:10088968 1/1:0,30:30:99:1|1:10088968_C_CAAA:1781,128,0:10088968 -20 10088980 . T C 3121.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.585e+00;DP=113;ExcessHet=3.0103;FS=2.621;MLEAC=3;MLEAF=0.750;MQ=54.22;MQRankSum=-5.232e+00;QD=27.87;ReadPosRankSum=1.29;SOR=0.917 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:37,31:68:99:0|1:10088968_C_CAAA:1276,0,1627:10088968 1/1:0,44:44:99:1|1:10088968_C_CAAA:1859,135,0:10088968 -20 10088985 . T C 3119.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.920e-01;DP=118;ExcessHet=3.0103;FS=3.545;MLEAC=3;MLEAF=0.750;MQ=54.16;MQRankSum=-5.248e+00;QD=26.66;ReadPosRankSum=1.23;SOR=0.889 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:42,32:74:99:0|1:10088968_C_CAAA:1207,0,1729:10088968 1/1:0,43:43:99:.:.:1926,132,0 +20 10088968 . C CAAA 2980.13 . AC=3;AF=0.750;AN=4;BaseQRankSum=0.552;DP=95;ExcessHet=3.0103;FS=1.907;MLEAC=3;MLEAF=0.750;MQ=55.48;MQRankSum=-4.750e+00;QD=31.67;ReadPosRankSum=2.42;SOR=1.012 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:30,23:53:99:0|1:10088968_C_CAAA:1213,0,1236:10088968 1/1:0,30:30:99:1|1:10088968_C_CAAA:1781,128,0:10088968 +20 10088980 . T C 3121.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.585e+00;DP=113;ExcessHet=3.0103;FS=2.621;MLEAC=3;MLEAF=0.750;MQ=54.22;MQRankSum=-5.232e+00;QD=27.87;ReadPosRankSum=1.29;SOR=0.917 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:37,31:68:99:0|1:10088968_C_CAAA:1276,0,1497:10088968 1/1:0,44:44:99:1|1:10088968_C_CAAA:1859,135,0:10088968 +20 10088985 . T C 3119.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.920e-01;DP=118;ExcessHet=3.0103;FS=3.545;MLEAC=3;MLEAF=0.750;MQ=54.16;MQRankSum=-5.248e+00;QD=26.66;ReadPosRankSum=1.23;SOR=0.889 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:42,32:74:99:0|1:10088968_C_CAAA:1207,0,1599:10088968 1/1:0,43:43:99:.:.:1926,132,0 20 10089149 . A G 1121.44 . AC=2;AF=0.500;AN=4;BaseQRankSum=1.75;ClippingRankSum=0.00;DP=114;ExcessHet=0.7918;FS=3.979;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=28.04;ReadPosRankSum=-4.740e-01;SOR=0.990 GT:AD:DP:GQ:PL 0/0:74,0:74:99:0,120,1800 1/1:1,39:40:99:1137,108,0 20 10089441 . A G 1199.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=-4.885e+00;DP=114;ExcessHet=3.0103;FS=6.071;MLEAC=1;MLEAF=0.250;MQ=59.70;MQRankSum=-9.480e-01;QD=15.79;ReadPosRankSum=-1.560e-01;SOR=1.363 GT:AD:DP:GQ:PL 0/1:37,39:76:99:1208,0,1313 0/0:38,0:38:99:0,102,1104 20 10089525 . C T 2915.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=5.86;DP=124;ExcessHet=3.0103;FS=7.522;MLEAC=3;MLEAF=0.750;MQ=59.66;MQRankSum=1.53;QD=23.51;ReadPosRankSum=0.862;SOR=0.754 GT:AD:DP:GQ:PL 0/1:38,43:81:99:1577,0,1088 1/1:0,43:43:99:1352,128,0 @@ -418,7 +418,7 @@ 20 10090970 . T C 1277.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=-4.840e-01;DP=113;ExcessHet=3.0103;FS=0.927;MLEAC=1;MLEAF=0.250;MQ=59.46;MQRankSum=1.51;QD=18.52;ReadPosRankSum=-7.200e-02;SOR=0.518 GT:AD:DP:GQ:PL 0/1:33,36:69:99:1286,0,1092 0/0:44,0:44:99:0,113,1448 20 10091214 . C T 1269.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.361;DP=114;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=59.73;MQRankSum=-9.160e-01;QD=18.14;ReadPosRankSum=-3.500e-02;SOR=0.625 GT:AD:DP:GQ:PL 0/1:33,37:70:99:1278,0,1110 0/0:44,0:44:99:0,113,1448 20 10091220 . A G 1219.44 . AC=2;AF=0.500;AN=4;DP=91;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=27.71;SOR=0.883 GT:AD:DP:GQ:PL 0/0:46,0:46:99:0,120,1800 1/1:0,44:44:99:1235,130,0 -20 10092415 . A G 1655.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=-6.731e+00;DP=140;ExcessHet=3.0103;FS=0.741;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=16.39;ReadPosRankSum=0.082;SOR=0.665 GT:AD:DP:GQ:PL 0/1:52,49:101:99:1664,0,1902 0/0:39,0:39:99:0,108,1239 +20 10092415 . A G 1655.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=-6.731e+00;DP=140;ExcessHet=3.0103;FS=0.741;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=16.39;ReadPosRankSum=0.082;SOR=0.665 GT:AD:DP:GQ:PL 0/1:52,49:101:99:1664,0,1901 0/0:39,0:39:99:0,108,1239 20 10092642 . T C 1412.44 . AC=2;AF=0.500;AN=4;DP=111;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;QD=27.69;SOR=0.732 GT:AD:DP:GQ:PL 0/0:60,0:60:99:0,120,1800 1/1:0,51:51:99:1428,151,0 20 10092927 . G T 126.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=-2.507e+00;DP=113;ExcessHet=3.0103;FS=60.191;MLEAC=1;MLEAF=0.250;MQ=59.37;MQRankSum=-3.009e+00;QD=1.76;ReadPosRankSum=-2.200e-01;SOR=5.279 GT:AD:DP:GQ:PL 0/1:59,13:72:99:135,0,1864 0/0:40,0:40:99:0,108,1608 20 10093568 . GT GTTT,G 1235.88 . AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=0.426;DP=87;ExcessHet=3.0103;FS=1.087;MLEAC=2,1;MLEAF=0.500,0.250;MQ=59.27;MQRankSum=0.410;QD=21.31;ReadPosRankSum=1.26;SOR=0.452 GT:AD:DP:GQ:PGT:PID:PL:PS 0/2:17,0,17:42:99:.:.:364,431,885,0,449,386 1/1:0,24,0:24:75:1|1:10093568_G_GTT:894,75,0,894,75,894:10093568 @@ -426,7 +426,7 @@ 20 10094251 . T A 1290.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=0.251;DP=99;ExcessHet=3.0103;FS=11.483;MLEAC=1;MLEAF=0.250;MQ=60.00;MQRankSum=0.00;QD=20.82;ReadPosRankSum=1.81;SOR=1.211 GT:AD:DP:GQ:PL 0/1:26,36:62:99:1299,0,781 0/0:37,0:37:99:0,100,1165 20 10094582 . A G 943.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=-1.388e+00;DP=106;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=59.39;MQRankSum=1.27;QD=13.68;ReadPosRankSum=-1.800e-02;SOR=0.772 GT:AD:DP:GQ:PL 0/1:39,30:69:99:952,0,1350 0/0:37,0:37:99:0,99,1130 20 10094774 . C T 1056.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=-7.840e-01;DP=124;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=59.69;MQRankSum=0.962;QD=14.09;ReadPosRankSum=0.197;SOR=0.690 GT:AD:DP:GQ:PL 0/1:40,35:75:99:1065,0,1282 0/0:49,0:49:97:0,97,1393 -20 10095432 . GTGATGATGA GTGA,G 2071.84 . AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=1.27;DP=112;ExcessHet=3.0103;FS=3.183;MLEAC=2,1;MLEAF=0.500,0.250;MQ=56.20;MQRankSum=-4.431e+00;QD=26.91;ReadPosRankSum=0.396;SOR=0.404 GT:AD:DP:GQ:PL 0/2:27,0,23:50:99:877,959,3140,0,2181,2108 1/1:0,27,0:27:82:1217,82,0,1217,82,1217 +20 10095432 . GTGATGATGA GTGA,G 2071.84 . AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=1.27;DP=112;ExcessHet=3.0103;FS=3.183;MLEAC=2,1;MLEAF=0.500,0.250;MQ=56.20;MQRankSum=-4.431e+00;QD=26.91;ReadPosRankSum=0.396;SOR=0.404 GT:AD:DP:GQ:PL 0/2:27,0,23:50:99:877,959,2030,0,1071,998 1/1:0,27,0:27:82:1217,82,0,1217,82,1217 20 10095741 . A G 1095.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=-5.340e-01;DP=105;ExcessHet=3.0103;FS=4.721;MLEAC=1;MLEAF=0.250;MQ=57.35;MQRankSum=-2.313e+00;QD=15.66;ReadPosRankSum=-5.000e-01;SOR=0.515 GT:AD:DP:GQ:PL 0/1:36,34:70:99:1104,0,1233 0/0:34,0:34:67:0,67,972 20 10096293 . C T 1375.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=4.66;DP=115;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.250;MQ=58.57;MQRankSum=1.40;QD=18.35;ReadPosRankSum=-1.135e+00;SOR=0.638 GT:AD:DP:GQ:PL 0/1:37,38:75:99:1384,0,1258 0/0:40,0:40:99:0,108,1181 20 10096357 . A G 1150.44 . AC=2;AF=0.500;AN=4;BaseQRankSum=0.964;ClippingRankSum=0.00;DP=101;ExcessHet=0.7918;FS=0.000;MLEAC=2;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=27.39;ReadPosRankSum=1.55;SOR=0.460 GT:AD:DP:GQ:PL 0/0:57,0:57:99:0,120,1800 1/1:1,41:42:94:1166,94,0 @@ -439,7 +439,7 @@ 20 10096933 . G C 3256.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=-1.914e+00;DP=123;ExcessHet=3.0103;FS=28.941;MLEAC=3;MLEAF=0.750;MQ=59.51;MQRankSum=-1.802e+00;QD=26.47;ReadPosRankSum=0.334;SOR=1.469 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:44,41:85:99:0|1:10096933_G_C:1540,0,1770:10096933 1/1:0,38:38:99:1|1:10096933_G_C:1730,117,0:10096933 20 10096958 . G A 3678.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=2.84;DP=139;ExcessHet=3.0103;FS=22.455;MLEAC=3;MLEAF=0.750;MQ=59.57;MQRankSum=-1.701e+00;QD=26.46;ReadPosRankSum=-1.833e+00;SOR=1.412 GT:AD:DP:GQ:PGT:PID:PL:PS 0|1:45,47:92:99:0|1:10096933_G_C:1795,0,1629:10096933 1/1:0,47:47:99:1|1:10096933_G_C:1897,141,0:10096933 20 10097075 . T G 2516.09 . AC=3;AF=0.750;AN=4;BaseQRankSum=1.82;ClippingRankSum=0.00;DP=126;ExcessHet=3.0103;FS=5.781;MLEAC=3;MLEAF=0.750;MQ=58.96;MQRankSum=0.00;QD=19.97;ReadPosRankSum=1.53;SOR=0.480 GT:AD:DP:GQ:PL 0/1:44,48:92:99:1474,0,1482 1/1:1,33:34:92:1056,92,0 -20 10097101 . C CTTTT,CTTT 2114.88 . AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=-1.134e+00;DP=104;ExcessHet=3.0103;FS=4.258;MLEAC=2,1;MLEAF=0.500,0.250;MQ=58.27;MQRankSum=-2.428e+00;QD=24.59;ReadPosRankSum=2.09;SOR=0.358 GT:AD:DP:GQ:PL 0/2:34,4,26:64:99:1129,558,2012,0,1324,1306 1/1:0,22,0:22:71:1008,71,0,1008,71,1009 +20 10097101 . C CTTTT,CTTT 2114.88 . AC=2,1;AF=0.500,0.250;AN=4;BaseQRankSum=-1.134e+00;DP=104;ExcessHet=3.0103;FS=4.258;MLEAC=2,1;MLEAF=0.500,0.250;MQ=58.27;MQRankSum=-2.428e+00;QD=24.59;ReadPosRankSum=2.09;SOR=0.358 GT:AD:DP:GQ:PL 0/2:34,4,26:64:99:1129,558,1826,0,1242,1259 1/1:0,22,0:22:71:1008,71,0,1008,71,1009 20 10097436 . CTTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTT C 1083.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=1.82;DP=119;ExcessHet=3.0103;FS=1.851;MLEAC=1;MLEAF=0.250;MQ=54.27;MQRankSum=-6.464e+00;QD=12.18;ReadPosRankSum=-3.097e+00;SOR=0.948 GT:AD:DP:GQ:PL 0/1:57,32:89:99:1092,0,2241 0/0:30,0:30:66:0,66,990 20 10097437 . TTTTCTTTCTTTCTTTCTTTCTTTCTTTCTTTC *,TTTTCTTTCTTTCTTTCTTTCTTTCTTTC,T 1843.28 . AC=1,1,2;AF=0.250,0.250,0.500;AN=4;DP=106;ExcessHet=3.0103;FS=0.000;MLEAC=1,1,2;MLEAF=0.250,0.250,0.500;MQ=55.40;QD=24.25;SOR=1.905 GT:AD:DP:GQ:PL 1/2:0,32,23,0:55:99:2127,940,1799,1195,0,1125,2201,1453,1262,2642 3/3:0,0,0,21:21:67:928,928,928,928,928,928,67,67,67,0 20 10097626 . C A 646.88 . AC=1;AF=0.250;AN=4;BaseQRankSum=1.09;DP=77;ExcessHet=3.0103;FS=2.701;MLEAC=1;MLEAF=0.250;MQ=58.24;MQRankSum=-1.331e+00;QD=13.48;ReadPosRankSum=1.02;SOR=0.324 GT:AD:DP:GQ:PL 0/1:28,20:48:99:655,0,957 0/0:29,0:29:81:0,81,1014 diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf.idx b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf.idx index b70c216f8e8..86255f54067 100644 Binary files a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf.idx and b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GenotypeGVCFs/newMQcalc.combined.genotyped.vcf.idx differ