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Removing Uniquify from main pipeline indel merge, since the pipeline isn't merging from samples with the same name anyway. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4721 348d0f76-0448-11de-a6fe-93d51630548a
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corin 2010-11-23 17:25:22 +00:00
parent 53672361cc
commit fe28f8da9c
1 changed files with 1 additions and 1 deletions
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2
scala/qscript/fullCallingPipeline.q
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@ -276,7 +276,7 @@ class fullCallingPipeline extends QScript {
val mergeIndels = new CombineVariants with CommandLineGATKArgs val mergeIndels = new CombineVariants with CommandLineGATKArgs
mergeIndels.jobOutputFile = new File(".queue/logs/IndelCalling/CombineVariants.out") mergeIndels.jobOutputFile = new File(".queue/logs/IndelCalling/CombineVariants.out")
mergeIndels.out = new TaggedFile("IndelCalls/" + qscript.pipeline.getProject.getName+".indels.vcf","vcf") mergeIndels.out = new TaggedFile("IndelCalls/" + qscript.pipeline.getProject.getName+".indels.vcf","vcf")
mergeIndels.genotypemergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.UNIQUIFY) mergeIndels.genotypemergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.UNSORTED)
mergeIndels.priority = priority mergeIndels.priority = priority
mergeIndels.variantmergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION) mergeIndels.variantmergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION)
mergeIndels.rodBind = indelCallFiles mergeIndels.rodBind = indelCallFiles