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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
This commit is contained in:
kshakir 2011-05-29 04:17:18 +00:00
parent b4d379584c
commit 8d294dd6e6
1 changed files with 2 additions and 2 deletions
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4
scala/qscript/playground/WholeGenomePipeline.scala
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@ -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"