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Minor updates to pacbio data processing script to make it work with the latest bwa version/settings.

This commit is contained in:
Ryan Poplin 2012-05-22 10:24:45 -04:00
parent 08dfd6cab6
commit c3fb321014
1 changed files with 3 additions and 0 deletions
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3
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
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@ -130,6 +130,7 @@ class PacbioProcessingPipeline extends QScript {
case class sortSam (inSam: File, outBam: File) extends SortSam with ExternalCommonArgs {
this.input = List(inSam)
this.output = outBam
this.memoryLimit = 8
this.sortOrder = SortOrder.coordinate
this.analysisName = queueLogDir + outBam + ".sortSam"
this.jobName = queueLogDir + outBam + ".sortSam"
@ -171,6 +172,7 @@ class PacbioProcessingPipeline extends QScript {
this.analysisName = queueLogDir + outRecalFile + ".covariates"
this.jobName = queueLogDir + outRecalFile + ".covariates"
this.scatterCount = threads
this.read_filter :+= "BadCigar"
}
case class recal (inBam: File, inRecalFile: File, outBam: File) extends TableRecalibration with CommandLineGATKArgs {
@ -182,6 +184,7 @@ class PacbioProcessingPipeline extends QScript {
this.isIntermediate = false
this.analysisName = queueLogDir + outBam + ".recalibration"
this.jobName = queueLogDir + outBam + ".recalibration"
this.read_filter :+= "BadCigar"
this.scatterCount = threads
}