From fe28f8da9c85f061ded543cafa2fe4f3a2949531 Mon Sep 17 00:00:00 2001 From: corin Date: Tue, 23 Nov 2010 17:25:22 +0000 Subject: [PATCH] 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 --- scala/qscript/fullCallingPipeline.q | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q index 7a700fdbf..49aaf1f65 100755 --- a/scala/qscript/fullCallingPipeline.q +++ b/scala/qscript/fullCallingPipeline.q @@ -276,7 +276,7 @@ class fullCallingPipeline extends QScript { val mergeIndels = new CombineVariants with CommandLineGATKArgs mergeIndels.jobOutputFile = new File(".queue/logs/IndelCalling/CombineVariants.out") 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.variantmergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION) mergeIndels.rodBind = indelCallFiles