From 6d809321d3d467d92f6c0552d8066e5d93324906 Mon Sep 17 00:00:00 2001 From: corin Date: Fri, 24 Dec 2010 03:06:50 +0000 Subject: [PATCH] Updating combien variants memory limit and dcov default for the full calling pipeline. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4907 348d0f76-0448-11de-a6fe-93d51630548a --- scala/qscript/fullCallingPipeline.q | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q index 43f359720..4b23c1ac7 100755 --- a/scala/qscript/fullCallingPipeline.q +++ b/scala/qscript/fullCallingPipeline.q @@ -34,7 +34,7 @@ class fullCallingPipeline extends QScript { var target_titv: Float = _ @Input(doc="per-sample downsampling level",shortName="dcov",required=false) - var downsampling_coverage = 300 + var downsampling_coverage = 600 @Input(doc="level of parallelism for IndelRealigner. By default is set to 1.", shortName="cleanerScatter", required=false) var num_cleaner_scatter_jobs = 1 @@ -292,7 +292,7 @@ class fullCallingPipeline extends QScript { mergeIndels.variantmergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION) mergeIndels.rodBind = indelCallFiles mergeIndels.analysisName = base+"_MergeIndels" - mergeIndels.memoryLimit = Some(16) + mergeIndels.memoryLimit = Some(4) mergeIndels.jobQueue = qscript.big_mem_queue // 1b. genomically annotate SNPs -- no longer slow