From c7e08965d067bb7e0ef325fa1338ca4c121d1a60 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Fri, 10 Jan 2014 01:36:39 -0500 Subject: [PATCH] The QD normalization for indels was busted and is now fixed. It is true that indels of length > 1 have higher QUALS than those of length = 1. But for the HC those QUALS are not that much higher, and it doesn't continue scaling up as the indels get larger. So we no longer normalize by indel length (which massively over-penalizes larger events and effectively drops their QD to 0). For the UG the previous normalization also wasn't perfect. Now we divide the indel length by a factor of 3 to make sure that QD is consistent over the range of indel lengths. Integration tests change because QD is different for indels. Also, got permission from Valentin to archive a failing test that no longer applies. Thanks to Kurt on the GATK forum for pointing this all out. --- .../gatk/walkers/annotator/QualByDepth.java | 22 ++++++++++++++++--- .../VariantAnnotatorIntegrationTest.java | 8 +++---- ...perGeneralPloidySuite1IntegrationTest.java | 6 ++--- ...perGeneralPloidySuite2IntegrationTest.java | 2 +- ...dGenotyperIndelCallingIntegrationTest.java | 16 +++++++------- .../UnifiedGenotyperIntegrationTest.java | 10 ++++----- ...GenotyperNormalCallingIntegrationTest.java | 4 ++-- ...dGenotyperReducedReadsIntegrationTest.java | 2 +- ...lexAndSymbolicVariantsIntegrationTest.java | 2 +- .../HaplotypeCallerGVCFIntegrationTest.java | 6 ++--- .../HaplotypeCallerIntegrationTest.java | 22 +++++++++---------- 11 files changed, 57 insertions(+), 43 deletions(-) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java index 906cfa021..106e4b443 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java @@ -108,7 +108,7 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati continue; depth += perReadAlleleLikelihoods.getNumberOfStoredElements(); - } else if (genotype.hasDP() && vc.isBiallelic()) { // TODO -- this currently only works with biallelic variants for now because multiallelics have had their PLs stripped out and therefore their qual score can't be recomputed + } else if ( genotype.hasDP() ) { depth += genotype.getDP(); } } @@ -117,13 +117,29 @@ public class QualByDepth extends InfoFieldAnnotation implements StandardAnnotati return null; final double altAlleleLength = GATKVariantContextUtils.getMeanAltAlleleLength(vc); - double QD = -10.0 * vc.getLog10PError() / ((double)depth * altAlleleLength); + // Hack: when refContext == null then we know we are coming from the HaplotypeCaller and do not want to do a + // full length-based normalization (because the indel length problem is present only in the UnifiedGenotyper) + double QD = -10.0 * vc.getLog10PError() / ((double)depth * indelNormalizationFactor(altAlleleLength, ref != null)); + + // Hack: see note in the fixTooHighQD method below QD = fixTooHighQD(QD); - Map map = new HashMap<>(); + + final Map map = new HashMap<>(); map.put(getKeyNames().get(0), String.format("%.2f", QD)); return map; } + /** + * Generate the indel normalization factor. + * + * @param altAlleleLength the average alternate allele length for the call + * @param increaseNormalizationAsLengthIncreases should we apply a normalization factor based on the allele length? + * @return a possitive double + */ + private double indelNormalizationFactor(final double altAlleleLength, final boolean increaseNormalizationAsLengthIncreases) { + return ( increaseNormalizationAsLengthIncreases ? Math.max(altAlleleLength / 3.0, 1.0) : 1.0); + } + /** * The haplotype caller generates very high quality scores when multiple events are on the * same haplotype. This causes some very good variants to have unusually high QD values, diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index 58c3bb9bd..7943eb09b 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -358,7 +358,7 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { final File outputVCFNoQD = executeTest("testQualByDepth calling without QD", specNoQD).getFirst().get(0); final String baseAnn = String.format("-T VariantAnnotator -R %s -V %s", REF, outputVCFNoQD.getAbsolutePath()) + " --no_cmdline_in_header -o %s -L 20:10130000-10134800 -A QualByDepth"; - final WalkerTestSpec specAnn = new WalkerTestSpec(baseAnn, 1, Arrays.asList("139a4384f5a7c1f49ada67f416642249")); + final WalkerTestSpec specAnn = new WalkerTestSpec(baseAnn, 1, Arrays.asList("0c331915b07b42d726bc3d623aa9997b")); specAnn.disableShadowBCF(); final File outputVCFAnn = executeTest("testQualByDepth re-annotation of QD", specAnn).getFirst().get(0); @@ -384,10 +384,8 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { Assert.assertFalse(lineAnn == null); final VariantContext vcAnn = codecAnn.decode(lineAnn); - if( vc.isBiallelic() ) { - Assert.assertTrue(vc.hasAttribute("QD")); - Assert.assertTrue(vcAnn.hasAttribute("QD")); - } + Assert.assertTrue(vc.hasAttribute("QD")); + Assert.assertTrue(vcAnn.hasAttribute("QD")); } Assert.assertFalse(lineIterator.hasNext()); diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java index 460b80121..5a16837f1 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite1IntegrationTest.java @@ -69,16 +69,16 @@ public class UnifiedGenotyperGeneralPloidySuite1IntegrationTest extends WalkerTe @Test(enabled = true) public void testBOTH_GGA_Pools() { - executor.PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_BOTH_GGA", "BOTH", "dac2d7969e109aee9ad2dad573759f58"); + executor.PC_LSV_Test(String.format(" -maxAltAlleles 2 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_BOTH_GGA", "BOTH", "0eec36459cf1f1e3e8739ab5b1cedb39"); } @Test(enabled = true) public void testINDEL_GGA_Pools() { - executor.PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_INDEL_GGA", "INDEL", "ceb105e3db0f2b993e3d725b0d60b6a3"); + executor.PC_LSV_Test(String.format(" -maxAltAlleles 1 -ploidy 24 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles %s", LSV_ALLELES), "LSV_INDEL_GGA", "INDEL", "73229442a8fe558e58dd5dd305eb2315"); } @Test(enabled = true) public void testINDEL_maxAltAlleles2_ploidy1_Pools_noRef() { - executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "4dd1b38f0389e339ce8a05956956aa8a"); + executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 1", "LSV_INDEL_DISC_NOREF_p1", "INDEL", "2787064918c7b391071a6ad4e5b0aba8"); } } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java index 48f36ccc6..4c8c12887 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperGeneralPloidySuite2IntegrationTest.java @@ -58,7 +58,7 @@ public class UnifiedGenotyperGeneralPloidySuite2IntegrationTest extends WalkerTe @Test(enabled = true) public void testINDEL_maxAltAlleles2_ploidy3_Pools_noRef() { - executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","39f559996f8d429839c585bbab68dbde"); + executor.PC_LSV_Test_NoRef(" -maxAltAlleles 2 -ploidy 3","LSV_INDEL_DISC_NOREF_p3","INDEL","50ebb7f74e5618acdd014dd87f2363fc"); } @Test(enabled = true) diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java index 6219eb578..deb0289c9 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIndelCallingIntegrationTest.java @@ -73,7 +73,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("3c8727ee6e2a6f10ab728c4869dd5b92")); + Arrays.asList("1ad3943ae27a0062c52a19abe1c0d32c")); executeTest(String.format("test indel caller in SLX"), spec); } @@ -88,7 +88,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { " -minIndelCnt 1" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("0cbe889e03bab6512680ecaebd52c536")); + Arrays.asList("9b4ead3da021763704fcb9d80a5ee6ff")); executeTest(String.format("test indel caller in SLX with low min allele count"), spec); } @@ -101,7 +101,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,500,000", 1, - Arrays.asList("e10c49fcf9a128745c2b050a52798e58")); + Arrays.asList("8a0a751afdb2a8166432d9822e4d814c")); executeTest(String.format("test indel calling, multiple technologies"), spec); } @@ -111,7 +111,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("475f8148123792064130faf9f9030fec")); + Arrays.asList("422a114943a9e3e9bf5872b82cbc6340")); executeTest("test MultiSample Pilot2 indels with alleles passed in", spec); } @@ -121,7 +121,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + privateTestDir + "indelAllelesForUG.vcf -I " + validationDataLocation + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, - Arrays.asList("a7e4e1bd128424d46cffdd538b220074")); + Arrays.asList("01fec03933816e8d82aabe6e5b276dd5")); executeTest("test MultiSample Pilot2 indels with alleles passed in and emitting all sites", spec); } @@ -136,7 +136,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -alleles " + result.get(0).getAbsolutePath() + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L " + result.get(0).getAbsolutePath(), 1, - Arrays.asList("903af514f70db9238064da311c4ea0de")); + Arrays.asList("e3c95f745ebf2d4f26759878966c5280")); executeTest("test MultiSample Pilot1 CEU indels using GENOTYPE_GIVEN_ALLELES", spec2); } @@ -176,7 +176,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { public void testMinIndelFraction0() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 0.0", 1, - Arrays.asList("d3721bee5edaa31fdd35edd7aa75feb3")); + Arrays.asList("4a45d5bd459565ec35c726894430e8df")); executeTest("test minIndelFraction 0.0", spec); } @@ -184,7 +184,7 @@ public class UnifiedGenotyperIndelCallingIntegrationTest extends WalkerTest { public void testMinIndelFraction25() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( assessMinIndelFraction + " -minIndelFrac 0.25", 1, - Arrays.asList("a5b6d7b32953500d936d3dff512a6254")); + Arrays.asList("a78c663eff00b28b44f368f03b2acf1b")); executeTest("test minIndelFraction 0.25", spec); } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index dcaed8bf2..b30d124c4 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -182,12 +182,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // -------------------------------------------------------------------------------------------------------------- @Test public void testHeterozyosity1() { - testHeterozosity( 0.01, "2f3051caa785c7c1e2a8b23fa4da90b1" ); + testHeterozosity( 0.01, "6053106407e09a6aefb78395a0e22ec4" ); } @Test public void testHeterozyosity2() { - testHeterozosity( 1.0 / 1850, "228df9e38580d8ffe1134da7449fa35e" ); + testHeterozosity( 1.0 / 1850, "37666375278259c4d7dc800a0f73c1ca" ); } private void testHeterozosity(final double arg, final String md5) { @@ -203,7 +203,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { // // -------------------------------------------------------------------------------------------------------------- - private final static String COMPRESSED_OUTPUT_MD5 = "eebec02fdde9937bffaf44902ace6207"; + private final static String COMPRESSED_OUTPUT_MD5 = "c5c6af421cffa12fe6bdaced6cd41dd2"; @Test public void testCompressedOutput() { @@ -260,7 +260,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -o %s" + " -L 1:10,000,000-10,100,000", 1, - Arrays.asList("c4248f02103e37e89b0f22c0d9c98492")); + Arrays.asList("630d1dcfb7650a9287d6723c38b0746a")); executeTest(String.format("test multiple technologies"), spec); } @@ -279,7 +279,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { " -L 1:10,000,000-10,100,000" + " -baq CALCULATE_AS_NECESSARY", 1, - Arrays.asList("96c7862d55e933b274cabe45c9c443d9")); + Arrays.asList("976e88e4accb4436ad9ac97df9477648")); executeTest(String.format("test calling with BAQ"), spec); } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java index 01aab8ae3..47ef49845 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperNormalCallingIntegrationTest.java @@ -88,7 +88,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testSingleSamplePilot2() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,100,000", 1, - Arrays.asList("02b521fe88a6606a29c12c0885c3debd")); + Arrays.asList("75503fce7521378f8c2170094aff29df")); executeTest("test SingleSample Pilot2", spec); } @@ -112,7 +112,7 @@ public class UnifiedGenotyperNormalCallingIntegrationTest extends WalkerTest{ public void testReverseTrim() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper --contamination_fraction_to_filter 0.05 --disableDithering -R " + b37KGReference + " --no_cmdline_in_header -glm INDEL -I " + validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam -o %s -L 20:10289124 -L 20:10090289", 1, - Arrays.asList("a973298b2801b80057bea88507e2858d")); + Arrays.asList("02c7804c8013ba1ead8e02b956b5e454")); executeTest("test reverse trim", spec); } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperReducedReadsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperReducedReadsIntegrationTest.java index 3b5690046..0a54acbe4 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperReducedReadsIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperReducedReadsIntegrationTest.java @@ -74,7 +74,7 @@ public class UnifiedGenotyperReducedReadsIntegrationTest extends WalkerTest { @Test public void testReducedBamINDELs() { - testReducedCalling("INDEL", "942930038cf7fc9a80b969461aaa9aa6"); + testReducedCalling("INDEL", "d593628b2bc144e987a9e75e5eee0001"); } diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java index 3907ffbd6..5769c3a51 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest.java @@ -64,7 +64,7 @@ public class HaplotypeCallerComplexAndSymbolicVariantsIntegrationTest extends Wa @Test public void testHaplotypeCallerMultiSampleComplex1() { - HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "88c10027c21712b1fe475c06cadd503c"); + HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "ff19ae39b0695680ea670d53f6f9ce47"); } private void HCTestSymbolicVariants(String bam, String args, String md5) { diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java index 97744f126..3f6151c71 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerGVCFIntegrationTest.java @@ -65,9 +65,9 @@ public class HaplotypeCallerGVCFIntegrationTest extends WalkerTest { final String WExIntervals = "-L 20:10,000,000-10,100,000 -isr INTERSECTION -L " + hg19Chr20Intervals; // this functionality can be adapted to provide input data for whatever you might want in your data - tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.NONE, PCRFreeIntervals, "3ce9c42e7e97a45a82315523dbd77fcf"}); - tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "c5a55196e10680a02c833a8a44733306"}); - tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "9b9923ef41bfc7346c905fdecf918f92"}); + tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.NONE, PCRFreeIntervals, "96328c91cf9b06de231b37a22a7a7639"}); + tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.BP_RESOLUTION, PCRFreeIntervals, "ac25e9a78b89655197513bb0eb7a6845"}); + tests.add(new Object[]{NA12878_PCRFREE, HaplotypeCaller.ReferenceConfidenceMode.GVCF, PCRFreeIntervals, "dc0dde72131d562587acae967cf2031f"}); tests.add(new Object[]{NA12878_WEx, HaplotypeCaller.ReferenceConfidenceMode.NONE, WExIntervals, "7cb1e431119df00ec243a6a115fa74b8"}); tests.add(new Object[]{NA12878_WEx, HaplotypeCaller.ReferenceConfidenceMode.BP_RESOLUTION, WExIntervals, "90e22230149e6c32d1115d0e2f03cab1"}); tests.add(new Object[]{NA12878_WEx, HaplotypeCaller.ReferenceConfidenceMode.GVCF, WExIntervals, "b39a4bc19a0acfbade22a011cd229262"}); diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java index dfbbd7084..ba296f263 100644 --- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java +++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java @@ -84,22 +84,22 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSample() { - HCTest(CEUTRIO_BAM, "", "c0b1b64c6005cd3640ffde5dbc10174b"); + HCTest(CEUTRIO_BAM, "", "f2ad35b5e0d181fb18da86a8971ce4f4"); } @Test public void testHaplotypeCallerSingleSample() { - HCTest(NA12878_BAM, "", "439ce9024f04aad08eab1526d887e295"); + HCTest(NA12878_BAM, "", "06abde3268336a7cdb21970f12e819ba"); } @Test public void testHaplotypeCallerGraphBasedSingleSample() { - HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "213df0bdaa78a695e9336128333e4407"); + HCTest(NA12878_BAM, "-likelihoodEngine GraphBased", "3d1cb9acdf66547f88ad1742e8178044"); } @Test public void testHaplotypeCallerGraphBasedMultiSample() { - HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "ceee711cac50b4bb66a084acb9264941"); + HCTest(CEUTRIO_BAM, "-likelihoodEngine GraphBased", "af6f1f504ad771201aedc0157de8830a"); } @Test(enabled = false) // can't annotate the rsID's yet @@ -110,7 +110,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerMultiSampleGGA() { HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf", - "b09437f11db40abd49195110e50692c2"); + "fd43de437bbaf960499f67daedc6ef63"); } @Test @@ -126,7 +126,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void testHaplotypeCallerSingleSampleIndelQualityScores() { - HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "c57c463542304fb7b2576e531faca89e"); + HCTestIndelQualityScores(NA12878_RECALIBRATED_BAM, "", "3a3bb5f0bcec603287520841c559638f"); } private void HCTestNearbySmallIntervals(String bam, String args, String md5) { @@ -173,7 +173,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { @Test public void HCTestProblematicReadsModifiedInActiveRegions() { final String base = String.format("-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965"; - final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("976463812534ac164a64c5d0c3ec988a")); + final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("170896ddcfe06ec47e08aefefd99cf78")); executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec); } @@ -244,7 +244,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestDBSNPAnnotationWGS() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-10,100,000 -D " + b37dbSNP132, 1, - Arrays.asList("a43d6226a51eb525f0774f88e3778189")); + Arrays.asList("6ab05a77d2e79d21ba85fadf844a13ba")); executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec); } @@ -261,7 +261,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestDBSNPAnnotationWGSGraphBased() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller -likelihoodEngine GraphBased --disableDithering --pcr_indel_model NONE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_PCRFREE + " -o %s -L 20:10,000,000-10,100,000 -D " + b37dbSNP132, 1, - Arrays.asList("a6c4d5d2eece2bd2c51a81e34e80040f")); + Arrays.asList("903af86b396ce88a6c8e4f4016fbe769")); executeTest("HC calling with dbSNP ID annotation on WGS intervals", spec); } @@ -293,7 +293,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestAggressivePcrIndelModelWGS() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering --pcr_indel_model AGGRESSIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,000,000-10,300,000", 1, - Arrays.asList("19c2992541ede7407192660fdc1fadbf")); + Arrays.asList("824188743703bc09225c5b9c6b404ac1")); executeTest("HC calling with aggressive indel error modeling on WGS intervals", spec); } @@ -301,7 +301,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestConservativePcrIndelModelWGS() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller --disableDithering --pcr_indel_model CONSERVATIVE -R " + b37KGReference + " --no_cmdline_in_header -I " + NA12878_BAM + " -o %s -L 20:10,000,000-10,300,000", 1, - Arrays.asList("f4ab037915db3a40ba26e9ee30d40e16")); + Arrays.asList("14de866430f49c0026aafc1e34ed8250")); executeTest("HC calling with conservative indel error modeling on WGS intervals", spec); } }