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Updated with new CombineVariants syntax 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5862 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2011-05-24 11:38:09 +00:00
parent 57e4693e4c
commit d551ce720d
2 changed files with 2 additions and 2 deletions
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2
scala/qscript/playground/HybridSelectionPipeline.scala
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@ -134,7 +134,7 @@ class HybridSelectionPipeline extends QScript {
combineSNPsIndels.rodBind :+= RodBind("indels", "VCF", filterIndels.out)
combineSNPsIndels.rodBind :+= RodBind("snps", "VCF", filterSNPs.out)
combineSNPsIndels.rod_priority_list = "indels,snps"
combineSNPsIndels.variantmergeoption = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION
combineSNPsIndels.filteredRecordsMergeType = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.FilteredRecordMergeType.UNION
combineSNPsIndels.assumeIdenticalSamples = true
combineSNPsIndels.out = projectBase + ".unannotated.vcf"
combineSNPsIndels.jobOutputFile = combineSNPsIndels.out + ".out"

2
scala/qscript/playground/WholeGenomePipeline.scala
View File

@ -158,7 +158,7 @@ class WholeGenomePipeline extends QScript {
val combineChunks = new CombineVariants with CommandLineGATKArgs
combineChunks.rodBind = chunkVcfs.zipWithIndex.map { case (vcf, index) => RodBind("input"+index, "VCF", vcf) }
combineChunks.rod_priority_list = chunkVcfs.zipWithIndex.map { case (vcf, index) => "input"+index }.mkString(",")
combineChunks.variantmergeoption = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION
combineChunks.filteredRecordsMergeType = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.FilteredRecordMergeType.UNION
combineChunks.assumeIdenticalSamples = true
combineChunks.out = projectBase + ".unfiltered.vcf"
combineChunks.jobOutputFile = combineChunks.out + ".out"