From 33ecec535d5a1f86ba399d611aca922f07f8fc5e Mon Sep 17 00:00:00 2001 From: Mark DePristo Date: Tue, 9 Apr 2013 09:52:56 -0400 Subject: [PATCH] Turn off the LD merging code by default -- It's just too hard to interpret the called variation when we merge variants via LD. -- Can now be turned on with -mergeVariantsViaLD -- Update MD5s --- .../gatk/walkers/haplotypecaller/HaplotypeCaller.java | 8 +++----- ...peCallerComplexAndSymbolicVariantsIntegrationTest.java | 2 +- .../haplotypecaller/HaplotypeCallerIntegrationTest.java | 2 +- 3 files changed, 5 insertions(+), 7 deletions(-) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java index c52892373..8a3cacdcd 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java @@ -282,8 +282,8 @@ public class HaplotypeCaller extends ActiveRegionWalker implem protected List annotationsToExclude = new ArrayList(Arrays.asList(new String[]{"SpanningDeletions", "TandemRepeatAnnotator"})); @Advanced - @Argument(fullName="dontMergeVariantsViaLD", shortName="dontMergeVariantsViaLD", doc="If specified, we will include low quality bases when doing the assembly", required = false) - protected boolean dontMergeVariantsViaLD = false; + @Argument(fullName="mergeVariantsViaLD", shortName="mergeVariantsViaLD", doc="If specified, we will merge variants together into block substitutions that are in strong local LD", required = false) + protected boolean mergeVariantsViaLD = false; /** * Which groups of annotations to add to the output VCF file. See the VariantAnnotator -list argument to view available groups. @@ -433,9 +433,7 @@ public class HaplotypeCaller extends ActiveRegionWalker implem likelihoodCalculationEngine = new LikelihoodCalculationEngine( (byte)gcpHMM, DEBUG, pairHMM ); - final MergeVariantsAcrossHaplotypes variantMerger = dontMergeVariantsViaLD - ? new MergeVariantsAcrossHaplotypes() - : new LDMerger(DEBUG, 10, 1); + final MergeVariantsAcrossHaplotypes variantMerger = mergeVariantsViaLD ? new LDMerger(DEBUG, 10, 1) : new MergeVariantsAcrossHaplotypes(); genotypingEngine = new GenotypingEngine( DEBUG, annotationEngine, USE_FILTERED_READ_MAP_FOR_ANNOTATIONS, variantMerger ); 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 ff2b3d0b6..d6fb3b70a 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 testHaplotypeCallerMultiSampleComplex() { - HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "80b9280b1e65952f60ba2fd738d4840f"); + HCTestComplexVariants(privateTestDir + "AFR.complex.variants.bam", "", "6b673efb6f12b5deebb3e63fe94c48ed"); } private void HCTestSymbolicVariants(String bam, String args, String md5) { 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 5fc8c5622..7b7f4d9cc 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 @@ -188,7 +188,7 @@ public class HaplotypeCallerIntegrationTest extends WalkerTest { public void HCTestReducedBam() { WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec( "-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1, - Arrays.asList("e30b974b038293841e6be23c93ce76e1")); + Arrays.asList("020b1a4feb82f050894f6066dc07cc4a")); executeTest("HC calling on a ReducedRead BAM", spec); }