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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
This commit is contained in:
corin 2010-12-24 03:06:50 +00:00
parent 6ebf5b30de
commit 6d809321d3
1 changed files with 2 additions and 2 deletions
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4
scala/qscript/fullCallingPipeline.q
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@ -34,7 +34,7 @@ class fullCallingPipeline extends QScript {
var target_titv: Float = _ var target_titv: Float = _
@Input(doc="per-sample downsampling level",shortName="dcov",required=false) @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) @Input(doc="level of parallelism for IndelRealigner. By default is set to 1.", shortName="cleanerScatter", required=false)
var num_cleaner_scatter_jobs = 1 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.variantmergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION)
mergeIndels.rodBind = indelCallFiles mergeIndels.rodBind = indelCallFiles
mergeIndels.analysisName = base+"_MergeIndels" mergeIndels.analysisName = base+"_MergeIndels"
mergeIndels.memoryLimit = Some(16) mergeIndels.memoryLimit = Some(4)
mergeIndels.jobQueue = qscript.big_mem_queue mergeIndels.jobQueue = qscript.big_mem_queue
// 1b. genomically annotate SNPs -- no longer slow // 1b. genomically annotate SNPs -- no longer slow