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Few organizational changes, queue output is now categorized and hidden. Also changed NA12878.Wex to dbsnp 129. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5290 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-02-22 22:49:38 +00:00
parent 8ea71fd294
commit ecfb51bcd8
1 changed files with 13 additions and 25 deletions
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38
scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
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@ -97,7 +97,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
val lowPass: Boolean = true
val targetDataSets: Map[String, Target] = Map(
"HiSeq" -> new Target("NA12878.HiSeq", hg18, dbSNP_hg18, hapmap_hg18,
"HiSeq" -> new Target("NA12878.HiSeq", hg18, dbSNP_hg18_129, hapmap_hg18,
"/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.indels.10.mask",
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam"),
new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.vcf"),
@ -182,29 +182,11 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.stand_emit_conf = Some( if ( t.isLowpass ) { 4.0 } else { 30.0 } )
this.input_file :+= t.bamList
this.out = t.rawVCF
this.baq = Some( if (noBAQ) {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF} else {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.RECALCULATE})
this.baq = Some( if (noBAQ) {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF} else {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY})
this.analysisName = t.name + "_UG"
this.jobName = t.name + ".snpcall"
if (t.dbsnpFile.endsWith(".rod")) this.DBSNP = new File(t.dbsnpFile)
else if (t.dbsnpFile.endsWith(".vcf")) this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
//todo -- beautify scattergather directory structure
/*
this.setupScatterFunction = {
case scatter: ScatterFunction =>
scatter.commandDirectory = new File("UG/ScatterGather")
scatter.jobOutputFile = new File(".queue/UG/ScatterGather/Scatter.out")
}
this.setupCloneFunction = {
case (clone: CloneFunction, index: Int) =>
clone.commandDirectory = new File("SnpCalls/ScatterGather/Scatter_%s".format(index))
clone.jobOutputFile = new File(".queue/logs/SNPCalling/ScatterGather/Scatter_%s.out".format(index))
}
this.setupGatherFunction = {
case (gather: GatherFunction, source: ArgumentSource) =>
gather.commandDirectory = new File("UG/ScatterGather/Gather_%s".format(source.field.getName))
gather.jobOutputFile = new File(".queue/UG/ScatterGather/Gather_%s.out".format(source.field.getName))
}
*/
}
// 2.) Filter SNPs
@ -217,6 +199,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.filterName ++= List("HARD_TO_VALIDATE")
this.filterExpression ++= List("\"MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1\"")
this.analysisName = t.name + "_VF"
this.jobName = t.name + ".filter"
if (!noMASK) {
this.rodBind :+= RodBind("mask", "Bed", t.maskFile)
this.maskName = "InDel"
@ -233,12 +216,13 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.filteredVCF } )
this.clusterFile = if ( goldStandard ) { t.goldStandardClusterFile } else { t.clusterFile }
this.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
this.analysisName = name + "_GVC"
this.intervalsString ++= List(t.intervals)
this.qual = Some(350) // clustering parameters to be updated soon pending new experimentation results
this.std = Some(3.5)
this.mG = Some(10)
this.ignoreFilter ++= FiltersToIgnore
this.analysisName = name + "_GVC"
this.jobName = t.name + ".cluster"
if (t.dbsnpFile.endsWith(".rod"))
this.DBSNP = new File(t.dbsnpFile)
else if (t.dbsnpFile.endsWith(".vcf"))
@ -271,6 +255,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.tranche ++= List("0.1", "1.0", "10.0", "100.0")
this.out = t.titvRecalibratedVCF
this.tranchesFile = t.titvTranchesFile
this.jobName = t.name + ".titv"
}
// 4b.) Choose VQSR tranches based on sensitivity to truth set
@ -282,17 +267,19 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.priorHapMap = Some(2.0)
this.prior1KG = Some(2.0)
this.tranchesFile = t.tsTranchesFile
this.jobName = t.name + ".nrs"
}
// 5.) Variant Cut filter out the variants marked by recalibration to the 99% tranche
class VariantCut(t: Target) extends ApplyVariantCuts with UNIVERSAL_GATK_ARGS {
this.reference_sequence = t.reference
this.rodBind :+= RodBind("input", "VCF", t.tsRecalibratedVCF )
this.analysisName = t.name + "_VC"
this.intervalsString ++= List(t.intervals)
this.out = t.cutVCF
this.tranchesFile = t.tsTranchesFile
this.fdr_filter_level = Some(1.0)
this.analysisName = t.name + "_VC"
this.jobName = t.name + ".cut"
if (t.dbsnpFile.endsWith(".rod"))
this.DBSNP = new File(t.dbsnpFile)
else if (t.dbsnpFile.endsWith(".vcf"))
@ -303,10 +290,11 @@ class MethodsDevelopmentCallingPipeline extends QScript {
class VariantEvaluation(t: Target) extends VariantEval with UNIVERSAL_GATK_ARGS {
val name: String = t.name
this.reference_sequence = t.reference
this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile)
this.knownName ++= List("hapmap")
this.rodBind :+= RodBind("comphapmap", "VCF", t.hapmapFile)
this.knownName ++= List("comphapmap")
this.rodBind :+= RodBind("eval", "VCF", if (!noCut) {t.cutVCF} else {t.tsRecalibratedVCF} )
this.analysisName = name + "_VE"
this.jobName = t.name + ".eval"
this.intervalsString ++= List(t.intervals)
this.EV ++= List("GenotypeConcordance")
this.out = t.evalFile