From d4cbd8691c2a7dd32f725ce579ed3ccfb1b90b93 Mon Sep 17 00:00:00 2001 From: ebanks Date: Tue, 3 May 2011 16:38:55 +0000 Subject: [PATCH] Make the default that we only output SNPs (so that when I make another release we don't get flooded with questions about why the UG is all of a sudden so slow) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5729 348d0f76-0448-11de-a6fe-93d51630548a --- .../genotyper/UnifiedArgumentCollection.java | 2 +- .../UnifiedGenotyperIntegrationTest.java | 25 +++++++++---------- .../UnifiedGenotyperPerformanceTest.java | 3 +++ 3 files changed, 16 insertions(+), 14 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java index 5d26b9e89..67be9cfea 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -36,7 +36,7 @@ public class UnifiedArgumentCollection { // control the various models to be used @Argument(fullName = "genotype_likelihoods_model", shortName = "glm", doc = "Genotype likelihoods calculation model to employ -- BOTH is the default option, while INDEL is also available for calling indels and SNP is available for calling SNPs only", required = false) - public GenotypeLikelihoodsCalculationModel.Model GLmodel = GenotypeLikelihoodsCalculationModel.Model.BOTH; + public GenotypeLikelihoodsCalculationModel.Model GLmodel = GenotypeLikelihoodsCalculationModel.Model.SNP; @Argument(fullName = "p_nonref_model", shortName = "pnrm", doc = "Non-reference probability calculation model to employ -- EXACT is the default option, while GRID_SEARCH is also available.", required = false) public AlleleFrequencyCalculationModel.Model AFmodel = AlleleFrequencyCalculationModel.Model.EXACT; 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 7b4244896..49c2459d8 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java @@ -16,7 +16,8 @@ import java.util.Map; public class UnifiedGenotyperIntegrationTest extends WalkerTest { - private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER"; + private final static String baseCommand = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm BOTH"; + private final static String baseCommandIndels = "-T UnifiedGenotyper -R " + b36KGReference + " -NO_HEADER -glm INDEL"; // -------------------------------------------------------------------------------------------------------------- // @@ -64,8 +65,8 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testSingleSamplePilot2() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -glm SNP -L 1:10,000,000-10,100,000", 1, - Arrays.asList("2241d97972b72233cb7b4c565739698e")); + 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("66e3fc85a6037a24bc2b4896f79ea263")); executeTest("test SingleSample Pilot2", spec); } @@ -242,10 +243,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testSimpleIndels() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - baseCommand + + baseCommandIndels + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam" + " -o %s" + - " -glm INDEL" + " -L 1:10,000,000-10,500,000", 1, Arrays.asList("84bc209f38d60f325f1a8b6292a82c82")); @@ -257,10 +257,10 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testIndelsWithLowMinAlleleCnt() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - baseCommand + + baseCommandIndels + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam" + " -o %s" + - " -glm INDEL -minIndelCnt 1" + + " -minIndelCnt 1" + " -L 1:10,000,000-10,100,000", 1, Arrays.asList("f536ca23cb86b14fc20e453859dafc01")); @@ -271,10 +271,9 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { @Test public void testMultiTechnologyIndels() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( - baseCommand + + baseCommandIndels + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam" + " -o %s" + - " -glm INDEL" + " -L 1:10,000,000-10,500,000", 1, Arrays.asList("e9b4fef2cdfa4c4657f0df53309131b6")); @@ -286,15 +285,15 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest { //@Test public void testWithIndelAllelesPassedIn() { WalkerTest.WalkerTestSpec spec1 = new WalkerTest.WalkerTestSpec( - baseCommand + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation + - "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000 -glm INDEL", 1, + baseCommandIndels + " --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation + + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, Arrays.asList("e95c545b8ae06f0721f260125cfbe1f0")); executeTest("test MultiSample Pilot2 indels with alleles passed in", spec1); WalkerTest.WalkerTestSpec spec2 = new WalkerTest.WalkerTestSpec( - baseCommand + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + baseCommandIndels + " --output_mode EMIT_ALL_SITES --genotyping_mode GENOTYPE_GIVEN_ALLELES -B:alleles,vcf " + validationDataLocation + "indelAllelesForUG.vcf -I " + validationDataLocation + - "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000 -glm INDEL", 1, + "pilot2_daughters.chr20.10k-11k.bam -o %s -L 20:10,000,000-10,100,000", 1, Arrays.asList("6c96d76b9bc3aade0c768d7c657ae210")); executeTest("test MultiSample Pilot2 indels with alleles passed in", spec2); } diff --git a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java index 4dc9f1ebb..866c27f8d 100755 --- a/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java +++ b/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperPerformanceTest.java @@ -12,6 +12,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-R " + hg18Reference + " -T UnifiedGenotyper" + + " -glm BOTH" + " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + " -L chr1:1-50,000,000" + " -D " + GATKDataLocation + "dbsnp_129_hg18.rod" + @@ -26,6 +27,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest { WalkerTestSpec spec = new WalkerTestSpec( "-R " + hg18Reference + " -T UnifiedGenotyper" + + " -glm BOTH" + " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" + " -L " + evaluationDataLocation + "whole_exome_agilent_designed_120.targets.chr1.interval_list" + " -D " + GATKDataLocation + "dbsnp_129_hg18.rod" + @@ -41,6 +43,7 @@ public class UnifiedGenotyperPerformanceTest extends WalkerTest { "-R " + hg18Reference + " -T UnifiedGenotyper" + " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + + " -glm BOTH" + " -L chr1:1-50,000,000" + " -nt 10" + " -D " + GATKDataLocation + "dbsnp_129_hg18.rod" +