From 8d294dd6e69289429da7c32f0946f8ca8cd2489a Mon Sep 17 00:00:00 2001 From: kshakir Date: Sun, 29 May 2011 04:17:18 +0000 Subject: [PATCH] For the snps to create combine snps and filtered indels, now using a VCF with just snps instead of vcf with snps plus unfiltered indels. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5904 348d0f76-0448-11de-a6fe-93d51630548a --- scala/qscript/playground/WholeGenomePipeline.scala | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scala/qscript/playground/WholeGenomePipeline.scala b/scala/qscript/playground/WholeGenomePipeline.scala index 49619b458..f8ebde6d0 100644 --- a/scala/qscript/playground/WholeGenomePipeline.scala +++ b/scala/qscript/playground/WholeGenomePipeline.scala @@ -188,8 +188,8 @@ class WholeGenomePipeline extends QScript { val combineSNPsIndels = new CombineVariants with CommandLineGATKArgs combineSNPsIndels.rodBind :+= RodBind("indels", "VCF", selectIndels.out) - combineSNPsIndels.rodBind :+= RodBind("all", "VCF", combineChunks.out) - combineSNPsIndels.rod_priority_list = "indels,all" + combineSNPsIndels.rodBind :+= RodBind("snps", "VCF", selectSNPs.out) + combineSNPsIndels.rod_priority_list = "indels,snps" combineSNPsIndels.filteredRecordsMergeType = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED combineSNPsIndels.assumeIdenticalSamples = true combineSNPsIndels.out = projectBase + ".unrecalibrated.vcf"