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quick and dirty 'close your eyes' solution to run the papuans over the weekend. Will be properly fixed soon. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5370 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-03-03 21:42:22 +00:00
parent f7ef35b8f5
commit 0daa65b9ef
1 changed files with 5 additions and 3 deletions
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8
scala/qscript/oneoffs/carneiro/dataProcessing.scala
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@ -27,10 +27,10 @@ class dataProcessing extends QScript {
var reference: File = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
@Input(doc="dbsnp ROD to use (VCF)", shortName="D", required=false)
val dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
@Input(doc="extra VCF files to use as reference indels for Indel Realignment", shortName="indels", required=false)
val indels: File = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/AFR+EUR+ASN+1KG.dindel_august_release_merged_pilot1.20110126.sites.vcf"
var indels: File = new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/AFR+EUR+ASN+1KG.dindel_august_release_merged_pilot1.20110126.sites.vcf")
@Input(doc="the project name determines the final output (BAM file) base name. Example NA12878 yields NA12878.processed.bam", shortName="p", required=false)
var projectName: String = "combined"
@ -145,11 +145,12 @@ class dataProcessing extends QScript {
this.targetIntervals = new File(tIntervals)
this.out = new File(outBam)
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
this.rodBind :+= RodBind("indels", "VCF", indels)
this.rodBind :+= RodBind("indels", "VCF", qscript.indels)
this.useOnlyKnownIndels = knownsOnly
this.doNotUseSW = true
this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY)
this.compress = Some(0)
this.U = Some(org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION) // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
this.isIntermediate = intermediate
this.jobName = queueLogDir + outBam + ".clean"
if (!intermediate && !qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
@ -184,6 +185,7 @@ class dataProcessing extends QScript {
this.input_file :+= new File (inBam)
this.recal_file = new File(inRecalFile)
this.out = new File(outBam)
this.U = Some(org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION) // todo -- update this with the last consensus between Tim, Matt and Eric. This is ugly!
this.index_output_bam_on_the_fly = Some(true)
this.jobName = queueLogDir + outBam + ".recalibration"
}