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fixed 1kg pilot dindel calls vcf file and combined all vcfs into one master dindel file. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5335 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-02-28 19:04:58 +00:00
parent e75366f738
commit c7a51f0de7
1 changed files with 5 additions and 20 deletions
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25
scala/qscript/oneoffs/carneiro/dataProcessing.scala
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@ -29,8 +29,8 @@ class dataProcessing extends QScript {
@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")
@Input(doc="extra VCF files to use as reference indels for Indel Realignment", shortName="indels", required=false) //todo -- once vcfs are merged, this will become the only indel vcf to be used and the merged file will be the default.
val indels: File = null
@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"
@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"
@ -44,13 +44,6 @@ class dataProcessing extends QScript {
@Input(doc="output bams at intervals only", shortName="intervals", required=false)
var intervals: File = _
// todo -- let's create a pre-merged single VCF and put it into /humgen/gsa-hpprojects/GATK/data please
val dindelPilotCalls: String = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg.pilot_release.merged.indels.sites.hg19.vcf"
val dindelAFRCalls: String = "/humgen/1kg/DCC/ftp/technical/working/20110126_dindel_august/AFR.dindel_august_release_merged_pilot1.20110126.sites.vcf.gz"
val dindelASNCalls: String = "/humgen/1kg/DCC/ftp/technical/working/20110126_dindel_august/ASN.dindel_august_release_merged_pilot1.20110126.sites.vcf.gz"
val dindelEURCalls: String = "/humgen/1kg/DCC/ftp/technical/working/20110126_dindel_august/EUR.dindel_august_release_merged_pilot1.20110126.sites.vcf.gz"
val queueLogDir: String = ".qlog/"
@ -134,15 +127,11 @@ class dataProcessing extends QScript {
this.out = new File(outIntervals)
this.mismatchFraction = Some(0.0)
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
this.rodBind :+= RodBind("indels1", "VCF", dindelPilotCalls)
this.rodBind :+= RodBind("indels2", "VCF", dindelAFRCalls)
this.rodBind :+= RodBind("indels3", "VCF", dindelEURCalls)
this.rodBind :+= RodBind("indels4", "VCF", dindelASNCalls)
if (qscript.indels != null) this.rodBind :+= RodBind("indels5", "VCF", qscript.indels)
this.rodBind :+= RodBind("indels", "VCF", indels)
}
class knownTargets (outIntervals: String) extends TargetBase {
class knownTargets (outIntervals: String) extends TargetBase(outIntervals) {
this.jobName = queueLogDir + outIntervals + ".ktarget"
}
@ -156,11 +145,7 @@ class dataProcessing extends QScript {
this.targetIntervals = new File(tIntervals)
this.out = new File(outBam)
this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
this.rodBind :+= RodBind("indels1", "VCF", dindelPilotCalls)
this.rodBind :+= RodBind("indels2", "VCF", dindelAFRCalls)
this.rodBind :+= RodBind("indels3", "VCF", dindelEURCalls)
this.rodBind :+= RodBind("indels4", "VCF", dindelASNCalls)
if (qscript.indels != null) this.rodBind :+= RodBind("indels5", "VCF", qscript.indels)
this.rodBind :+= RodBind("indels", "VCF", indels)
this.useOnlyKnownIndels = knownsOnly
this.doNotUseSW = true
this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY)