From 7055a3ea2d7b9d041044e15572db3685ce36da7f Mon Sep 17 00:00:00 2001 From: ebanks Date: Wed, 2 Dec 2009 17:24:06 +0000 Subject: [PATCH] - All annotations are now required to return their VCF INFO keys and descriptions - Renamed keys to fit with the standard naming - FisherStrand is no longer standard - Integration tests no longer test experimental annotations since they're not stable git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2216 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/annotator/AlleleBalance.java | 6 +++++- .../gatk/walkers/annotator/DepthOfCoverage.java | 6 +++++- .../gatk/walkers/annotator/FisherStrand.java | 8 ++++++-- .../gatk/walkers/annotator/HomopolymerRun.java | 6 +++++- .../walkers/annotator/MappingQualityZero.java | 6 +++++- .../PrimaryBaseSecondaryBaseSymmetry.java | 4 ++++ .../walkers/annotator/RMSMappingQuality.java | 6 +++++- .../gatk/walkers/annotator/RankSumTest.java | 6 +++++- .../gatk/walkers/annotator/ResidualQuality.java | 4 ++++ .../gatk/walkers/annotator/SecondBaseSkew.java | 4 ++++ .../walkers/annotator/SpanningDeletions.java | 6 +++++- .../walkers/annotator/VariantAnnotation.java | 2 ++ .../gatk/walkers/annotator/VariantAnnotator.java | 2 +- .../VariantAnnotatorIntegrationTest.java | 16 ++++++++-------- .../UnifiedGenotyperIntegrationTest.java | 12 ++++++------ packages/GenomeAnalysisTK.xml | 1 - 16 files changed, 70 insertions(+), 25 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java index 14da1e077..0036572a3 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java @@ -40,9 +40,13 @@ public class AlleleBalance extends StandardVariantAnnotation { ratio = computeSingleBalance(ref.getBase(), genotypeStr, bases); } - return new Pair("AlleleBalance", String.format("%.2f", ratio)); + return new Pair(getKeyName(), String.format("%.2f", ratio)); } + public String getKeyName() { return "AB"; } + + public String getDescription() { return "AB,1,Float,\"Allele Balance (ref/(ref+alt))\""; } + private double computeSingleBalance(char ref, final String genotypeStr, final String bases) { char a = genotypeStr.charAt(0); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java index 504b56d97..93c4002f9 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java @@ -13,8 +13,12 @@ public class DepthOfCoverage extends StandardVariantAnnotation { public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List genotypes) { int depth = pileup.getReads().size(); - return new Pair("DoC", String.format("%d", depth)); + return new Pair(getKeyName(), String.format("%d", depth)); } + public String getKeyName() { return "DP"; } + + public String getDescription() { return "DP,1,Integer,\"Total Depth\""; } + public boolean useZeroQualityReads() { return false; } } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java index 0cbf43642..017c0fead 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java @@ -12,7 +12,7 @@ import cern.jet.math.Arithmetic; import java.util.List; -public class FisherStrand extends StandardVariantAnnotation { +public class FisherStrand implements VariantAnnotation { public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List genotypes) { @@ -33,9 +33,13 @@ public class FisherStrand extends StandardVariantAnnotation { return null; // use Math.abs to prevent -0's - return new Pair("FisherStrand", String.format("%.1f", Math.abs(10.0 * Math.log10(pvalue)))); + return new Pair(getKeyName(), String.format("%.1f", Math.abs(10.0 * Math.log10(pvalue)))); } + public String getKeyName() { return "FisherStrand"; } + + public String getDescription() { return "FisherStrand,1,Float,\"Phred-scaled p-value Using Fisher's Exact Test to Detect Strand Bias\""; } + public boolean useZeroQualityReads() { return false; } private Double strandTest(ReadBackedPileup pileup, int allele1, int allele2) { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java index a43689b06..d6db5e615 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java @@ -18,9 +18,13 @@ public class HomopolymerRun extends StandardVariantAnnotation { return null; int run = computeHomopolymerRun(variation.getAlternativeBaseForSNP(), ref); - return new Pair("HomopolymerRun", String.format("%d", run)); + return new Pair(getKeyName(), String.format("%d", run)); } + public String getKeyName() { return "HRun"; } + + public String getDescription() { return "HRun,1,Integer,\"Largest Contiguous Homopolymer Run of Variant Allele In Either Direction\""; } + public boolean useZeroQualityReads() { return false; } private static int computeHomopolymerRun(char altAllele, ReferenceContext ref) { diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java index 6e465a279..36edd3880 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java @@ -19,8 +19,12 @@ public class MappingQualityZero extends StandardVariantAnnotation { if ( reads.get(i).getMappingQuality() == 0 ) MQ0Count++; } - return new Pair("MAPQ0", String.format("%d", MQ0Count)); + return new Pair(getKeyName(), String.format("%d", MQ0Count)); } + public String getKeyName() { return "MQ0"; } + + public String getDescription() { return "MQ0,1,Integer,\"Total Mapping Quality Zero Reads\""; } + public boolean useZeroQualityReads() { return true; } } \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/PrimaryBaseSecondaryBaseSymmetry.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/PrimaryBaseSecondaryBaseSymmetry.java index 7cce56074..f4e4a2daf 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/PrimaryBaseSecondaryBaseSymmetry.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/PrimaryBaseSecondaryBaseSymmetry.java @@ -51,6 +51,10 @@ public class PrimaryBaseSecondaryBaseSymmetry implements VariantAnnotation{ } } + public String getKeyName() { return KEY_NAME; } + + public String getDescription() { return KEY_NAME + ",1,Float,\"Primary Vs. Secondary Base Symmetry\""; } + private Pair getProportionOfReferenceSecondBasesThatSupportAlt( ReferenceContext ref, ReadBackedPileup p, byte snp ) { int depth = 0; int support = 0; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java index 242bf3f60..253ad6eb1 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java @@ -19,8 +19,12 @@ public class RMSMappingQuality extends StandardVariantAnnotation { for (int i=0; i < reads.size(); i++) qualities[i] = reads.get(i).getMappingQuality(); double rms = MathUtils.rms(qualities); - return new Pair("RMSMAPQ", String.format("%.2f", rms)); + return new Pair(getKeyName(), String.format("%.2f", rms)); } + public String getKeyName() { return "MQ"; } + + public String getDescription() { return "MQ,1,Float,\"RMS Mapping Quality\""; } + public boolean useZeroQualityReads() { return true; } } \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java index ccc6618a1..0949da0f6 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java @@ -40,9 +40,13 @@ public class RankSumTest implements VariantAnnotation { if ( MathUtils.compareDoubles(pvalue, 0.0) == 0 ) return null; - return new Pair("RankSum", String.format("%.1f", -10.0 * Math.log10(pvalue))); + return new Pair(getKeyName(), String.format("%.1f", -10.0 * Math.log10(pvalue))); } + public String getKeyName() { return "RankSum"; } + + public String getDescription() { return "RankSum,1,Float,\"Phred-scaled p-value From Wilcoxon Rank Sum Test of Het Vs. Ref Base Qualities\""; } + private void fillQualsFromPileup(char ref, char alt, ReadBackedPileup pileup, List refQuals, List altQuals) { for ( PileupElement p : pileup ) { // ignore deletions diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ResidualQuality.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ResidualQuality.java index c37ccca7b..9367b31e3 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ResidualQuality.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ResidualQuality.java @@ -38,6 +38,10 @@ public class ResidualQuality implements VariantAnnotation{ return new Pair(KEY_NAME, String.format("%f", logResidQual )); } + public String getKeyName() { return KEY_NAME; } + + public String getDescription() { return KEY_NAME + ",1,Float,\"Log-scaled Residual Error\""; } + private Double getLogResidualQuality( ReadBackedPileup p, char ref, char snp ) { byte[] pbp = p.getBases(); byte[] quals = p.getQuals(); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java index 0b581e3f6..15f2c2aeb 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SecondBaseSkew.java @@ -26,6 +26,10 @@ public class SecondBaseSkew implements VariantAnnotation { public boolean useZeroQualityReads() { return USE_ZERO_QUALITY_READS; } + public String getKeyName() { return KEY_NAME; } + + public String getDescription() { return KEY_NAME + ",1,Float,\"Chi-square Secondary Base Skew\""; } + public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List genotypes) { if ( variation.isSNP() && variation.isBiallelic() ) { char snp = variation.getAlternativeBaseForSNP(); diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java index 0df3ee4a2..759cf3a51 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java @@ -13,8 +13,12 @@ public class SpanningDeletions extends StandardVariantAnnotation { public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List genotypes) { int deletions = pileup.getNumberOfDeletions(); - return new Pair("SpanningDeletionFraction", String.format("%.2f", (double)deletions/(double)pileup.size())); + return new Pair(getKeyName(), String.format("%.2f", (double)deletions/(double)pileup.size())); } + public String getKeyName() { return "Dels"; } + + public String getDescription() { return "Dels,1,Float,\"Fraction of Reads Containing Spanning Deletions\""; } + public boolean useZeroQualityReads() { return false; } } \ No newline at end of file diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotation.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotation.java index ff294fdc5..51d8c1ab6 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotation.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotation.java @@ -12,5 +12,7 @@ public interface VariantAnnotation { public Pair annotate(ReferenceContext ref, ReadBackedPileup pileup, Variation variation, List genotypes); public boolean useZeroQualityReads(); + public String getKeyName(); + public String getDescription(); } diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java index 2925365d0..a629ffac6 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java @@ -28,7 +28,7 @@ public class VariantAnnotator extends RodWalker { protected String sampleName = null; @Argument(fullName="annotations", shortName="A", doc="Annotation types to apply to variant calls", required=false) protected String[] ANNOTATIONS; - @Argument(fullName="useAllAnnotations", shortName="all", doc="Use all possible annotations", required=false) + @Argument(fullName="includeExperimentalAnnotations", shortName="exp", doc="Use all possible annotations, including experimental ones", required=false) protected Boolean USE_ALL_ANNOTATIONS = false; @Argument(fullName="useStandardAnnotations", shortName="standard", doc="Use all standard annotations", required=false) protected Boolean USE_STANDARD_ANNOTATIONS = false; diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java index 1a8fedb31..e2495f6e5 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorIntegrationTest.java @@ -65,16 +65,16 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testHasAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -all -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("aa4fd832eab85123b97c7961c9c8402a")); + baseTestString() + " -standard -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, + Arrays.asList("9a30487ad885f4d49569032fe6463af3")); executeTest("test file has annotations, asking for annotations, #1", spec); } @Test public void testHasAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -all -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample3.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, - Arrays.asList("fcae8ca66020be99cc01cc699f489462")); + baseTestString() + " -standard -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample3.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, + Arrays.asList("ef01d735ea0bcfeb6e7394c65f2a1938")); executeTest("test file has annotations, asking for annotations, #2", spec); } @@ -97,16 +97,16 @@ public class VariantAnnotatorIntegrationTest extends WalkerTest { @Test public void testNoAnnotsAsking1() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -all -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2empty.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, - Arrays.asList("ad3945cab44444d3b1c0bd35307814f7")); + baseTestString() + " -standard -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample2empty.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -L 1:10,020,000-10,021,000", 1, + Arrays.asList("7e6ceb79e9a1f104723299ed68b236c6")); executeTest("test file doesn't have annotations, asking for annotations, #1", spec); } @Test public void testNoAnnotsAsking2() { WalkerTestSpec spec = new WalkerTestSpec( - baseTestString() + " -all -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample3empty.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, - Arrays.asList("c31832ce6abf496180ebb64c1916b2e8")); + baseTestString() + " -standard -B variant,VCF,/humgen/gsa-scr1/GATK_Data/Validation_Data/vcfexample3empty.vcf -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -L 1:10,000,000-10,050,000", 1, + Arrays.asList("87748d4c80ff76701dd01d7b0f803249")); executeTest("test file doesn't have annotations, asking for annotations, #2", spec); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java index be93cb191..fda9aac5f 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -47,7 +47,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSamplePilot1PointEM() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,400-10,024,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1, - Arrays.asList("b14783b877e4857366cf9b1f516de343")); + Arrays.asList("e401eb288c167b72f2fb3d0b3f9c22da")); executeTest("testMultiSamplePilot1 - Point Estimate EM", spec); } @@ -55,7 +55,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSamplePilot2PointEM() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,010,000 -bm empirical -gm EM_POINT_ESTIMATE -confidence 30", 1, - Arrays.asList("72bcbd0786bb94803d1ad867becf12e2")); + Arrays.asList("ce9f37df3275ed4e7abaedf33d982889")); executeTest("testMultiSamplePilot2 - Point Estimate EM", spec); } @@ -68,7 +68,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testPooled1() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,023,000-10,024,000 -bm empirical -gm POOLED -ps 60 -confidence 30", 1, - Arrays.asList("48f17694db2fc8744741e4eb73227e5b")); + Arrays.asList("1905bc65b1abb56c776558d562de5ea1")); executeTest("testPooled1", spec); } @@ -81,7 +81,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSamplePilot1Joint() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/low_coverage_CEU.chr1.10k-11k.bam -varout %s -L 1:10,022,000-10,025,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1, - Arrays.asList("e72379c9654db9cf6ee17e7b9126f23e")); + Arrays.asList("aaecb9fe822a42576500a91973baff03")); executeTest("testMultiSamplePilot1 - Joint Estimate", spec); } @@ -89,7 +89,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testMultiSamplePilot2Joint() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/pilot2_daughters.chr20.10k-11k.bam -varout %s -L 20:10,000,000-10,050,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1, - Arrays.asList("577ad8a1b1d16efc68e833a6d8e5b638")); + Arrays.asList("d36a8ba5ddf1265ab5be2ed390fa56e1")); executeTest("testMultiSamplePilot2 - Joint Estimate", spec); } @@ -97,7 +97,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { public void testSingleSamplePilot2Joint() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T UnifiedGenotyper -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -varout %s -L 1:10,000,000-10,100,000 -bm empirical -gm JOINT_ESTIMATE -confidence 30", 1, - Arrays.asList("b4a18843fc6fa76a878c39dfde1cedda")); + Arrays.asList("029706a60440660c6a636091e9489122")); executeTest("testSingleSamplePilot2 - Joint Estimate", spec); } diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml index f7658ac98..a4c9c34d2 100644 --- a/packages/GenomeAnalysisTK.xml +++ b/packages/GenomeAnalysisTK.xml @@ -40,7 +40,6 @@ org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage - org.broadinstitute.sting.gatk.walkers.annotator.FisherStrand org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun org.broadinstitute.sting.gatk.walkers.annotator.MappingQualityZero org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality