zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

4
scala/qscript/fullCallingPipeline.q
View File

@ -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