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NO BAQ ON EXOMES! 

says the boss.
This commit is contained in:
Mauricio Carneiro 2011-09-22 11:13:40 -04:00
parent 96768c8a18
commit 623c49765d
1 changed files with 1 additions and 1 deletions
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2
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
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@ -221,7 +221,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.max_deletion_fraction = qscript.deletions
this.out = t.rawVCF
this.glm = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.SNP
this.baq = if (noBAQ) {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF} else {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY}
this.baq = if (noBAQ || t.isExome) {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF} else {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY}
this.analysisName = t.name + "_UGs"
this.jobName = queueLogDir + t.name + ".snpcall"
}