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Adjusting the memory limits of the MDCP 

Indel caller needs more than 3G for large datasets.
This commit is contained in:
Mauricio Carneiro 2011-10-21 17:41:52 -04:00
parent 102dafdcbc
commit 86305a5dcf
1 changed files with 1 additions and 2 deletions
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3
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
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@ -205,7 +205,6 @@ class MethodsDevelopmentCallingPipeline extends QScript {
// 1.) Unified Genotyper Base
class GenotyperBase (t: Target) extends UnifiedGenotyper with UNIVERSAL_GATK_ARGS {
this.memoryLimit = 3
this.reference_sequence = t.reference
this.intervalsString ++= List(t.intervals)
this.scatterCount = 140
@ -232,6 +231,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
// 1b.) Call Indels with UG
class indelCall (t: Target) extends GenotyperBase(t) {
this.memoryLimit = 6
this.out = t.rawIndelVCF
this.glm = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.INDEL
this.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF
@ -259,7 +259,6 @@ class MethodsDevelopmentCallingPipeline extends QScript {
// 3.) Variant Quality Score Recalibration - Generate Recalibration table
class VQSR(t: Target, goldStandard: Boolean) extends VariantRecalibrator with UNIVERSAL_GATK_ARGS {
this.memoryLimit = 4
this.nt = 2
this.reference_sequence = t.reference
this.intervalsString ++= List(t.intervals)