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- minor changes to the 'justclean' script to handle the Trio Cleaning. 

- fixing a bug on single ended BWA option of the data processing pipeline.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5662 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-04-19 16:35:24 +00:00
parent 49550e257f
commit d35c7d1029
2 changed files with 5 additions and 5 deletions
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2
scala/qscript/oneoffs/carneiro/dataProcessingV2.scala
View File

@ -442,7 +442,7 @@ class dataProcessingV2 extends QScript {
@Input(doc="bwa alignment index file for 1st mating pair") var sai1 = inSai1
@Input(doc="bwa alignment index file for 2nd mating pair") var sai2 = inSai2
@Output(doc="output aligned bam file") var alignedBam = outBam
def commandLine = bwaPath + " samse " + reference + " " + sai1 + " " + sai2 + " " + bam + " -r " + readGroup + " > " + alignedBam
def commandLine = bwaPath + " sampe " + reference + " " + sai1 + " " + sai2 + " " + bam + " -r " + readGroup + " > " + alignedBam
this.isIntermediate = true
this.analysisName = queueLogDir + outBam + ".bwa_sam_pe"
this.jobName = queueLogDir + outBam + ".bwa_sam_pe"

8
scala/qscript/oneoffs/carneiro/justClean.scala
View File

@ -59,14 +59,14 @@ class justClean extends QScript {
clean.reference_sequence = reference
clean.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
clean.rodBind :+= RodBind("indels", "VCF", indels)
clean.doNotUseSW = true
clean.doNotUseSW = false
clean.compress = 0
clean.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update clean with the last consensus between Tim, Matt and Eric. This is ugly!
// clean.U = org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION // todo -- update clean with the last consensus between Tim, Matt and Eric. This is ugly!
clean.jobName = queueLogDir + outBam + ".clean"
clean.jarFile = GATKjar
clean.memoryLimit = 12
clean.memoryLimit = 6
clean.scatterCount = 84
add(clean);
add(target, clean);
}
}