From f0ab7b849a7cca93b15509fd8ef872783553e2ed Mon Sep 17 00:00:00 2001 From: corin Date: Sat, 18 Dec 2010 04:19:54 +0000 Subject: [PATCH] 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 --- scala/qscript/fullCallingPipeline.q | 1 + 1 file changed, 1 insertion(+) diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q index d4ee7f4c2..324b378b1 100755 --- a/scala/qscript/fullCallingPipeline.q +++ b/scala/qscript/fullCallingPipeline.q @@ -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")