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Adding a window size variable to avoid indel genotyper error 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4873 348d0f76-0448-11de-a6fe-93d51630548a
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corin 2010-12-18 04:19:54 +00:00
parent a3729bd59c
commit f0ab7b849a
1 changed files with 1 additions and 0 deletions
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scala/qscript/fullCallingPipeline.q
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@ -256,6 +256,7 @@ class fullCallingPipeline extends QScript {
var indel = new IndelGenotyperV2 with CommandLineGATKArgs
indel.jobOutputFile = new File(".queue/logs/IndelCalling/%s/IndelGenotyperV2.out".format(sampleId))
indel.window_size = Some(350)
indel.analysisName = "IndelGenotyper_"+sampleId
indel.input_file :+= bam
indel.out = swapExt("IndelCalls/IntermediateFiles/" + sampleId, bam,".bam",".indels.vcf")