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DPP: Updated after some tests with BWA. Still needs more testing. 

MDP: Removed ApplyVariantCut as it's no longer necessary with VQSR2.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5534 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-03-29 18:22:09 +00:00
parent f6dfdc7f3b
commit c3f70cc5cb
2 changed files with 12 additions and 34 deletions
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24
scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
View File

@ -38,9 +38,6 @@ class MethodsDevelopmentCallingPipeline extends QScript {
@Argument(shortName="eval", doc="adds the VariantEval walker to the pipeline", required=false)
var eval: Boolean = false
@Argument(shortName="noCut", doc="removes the ApplyVariantCut walker from the pipeline", required=false)
var noCut: Boolean = false
@Argument(shortName="indels", doc="calls indels with the Unified Genotyper", required=false)
var callIndels: Boolean = false
@ -81,7 +78,6 @@ class MethodsDevelopmentCallingPipeline extends QScript {
val goldStandardRecalibratedVCF = new File(name + "goldStandard.recalibrated.vcf")
val goldStandardTranchesFile = new File(name + "goldStandard.tranches")
val goldStandardRecalFile = new File(name + "goldStandard.tranches.recal")
val cutVCF = new File(name + ".cut.vcf")
val evalFile = new File(name + ".snp.eval")
val evalIndelFile = new File(name + ".indel.eval")
val goldStandardName = qscript.outputDir + "goldStandard/" + baseName
@ -171,7 +167,6 @@ class MethodsDevelopmentCallingPipeline extends QScript {
add(new snpCall(target))
add(new VQSR(target, !goldStandard))
add(new applyVQSR(target, !goldStandard))
if (!noCut) add(new VariantCut(target))
if (eval) add(new snpEvaluation(target))
}
if ( !skipGoldStandard ) {
@ -285,23 +280,6 @@ class MethodsDevelopmentCallingPipeline extends QScript {
}
// 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.recalibratedVCF )
this.intervalsString ++= List(t.intervals)
this.out = t.cutVCF
this.tranchesFile = t.tranchesFile
this.fdr_filter_level = t.trancheTarget
if (t.dbsnpFile.endsWith(".rod"))
this.DBSNP = new File(t.dbsnpFile)
else if (t.dbsnpFile.endsWith(".vcf"))
this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
this.analysisName = t.name + "_VC"
this.jobName = queueLogDir + t.name + ".cut"
}
// 6.) Variant Evaluation Base(OPTIONAL)
class EvalBase(t: Target) extends VariantEval with UNIVERSAL_GATK_ARGS {
this.reference_sequence = t.reference
@ -317,7 +295,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
// 6a.) SNP Evaluation (OPTIONAL) based on the cut vcf
class snpEvaluation(t: Target) extends EvalBase(t) {
if (t.reference == b37 || t.reference == hg19) this.rodBind :+= RodBind("compomni", "VCF", omni_b37)
this.rodBind :+= RodBind("eval", "VCF", if (useCut) {t.cutVCF} else {t.recalibratedVCF} )
this.rodBind :+= RodBind("eval", "VCF", t.recalibratedVCF )
this.out = t.evalFile
this.analysisName = t.name + "_VEs"
this.jobName = queueLogDir + t.name + ".snp.eval"

22
scala/qscript/oneoffs/carneiro/dataProcessingV2.scala
View File

@ -162,16 +162,16 @@ class dataProcessingV2 extends QScript {
// Takes a list of processed BAM files, revert them to unprocessed and realigns each lane, producing a list of
// per-lane aligned bam files, ready to be processed.
def performAlignment(bamFiles: List[File]): List[File] = {
def performAlignment(bamList: File): List[File] = {
return List()
}
def createListFromFile(in: File):List[File] = {
if (in.toString.endsWith("bam"))
return List(in)
val l: List[File] = List()
var l: List[File] = List()
for (bam <- fromFile(in).getLines)
l :+= bam
l :+= new File(bam)
return l
}
@ -185,7 +185,7 @@ class dataProcessingV2 extends QScript {
def script = {
//todo -- (option - BWA) run BWA on each bam file (per lane bam file) before performing per sample processing
val perLaneAlignedBamFiles: List[File] = if (useBWApe || useBWAse) {performAlignment(input)} else {createListFromFile(input)}
val perLaneAlignedBamFiles: List[File] = if (useBWApe || useBWAse) { performAlignment(input) } else { createListFromFile(input) }
// Generate a BAM file per sample joining all per lane files if necessary
val sampleBamFiles = createSampleFiles(perLaneAlignedBamFiles)
@ -360,7 +360,7 @@ class dataProcessingV2 extends QScript {
}
case class sortSam (inSam: File, outBam: File) extends PicardBamFunction {
@Input(doc="input unsorted sam file") var sam = inBams
@Input(doc="input unsorted sam file") var sam = inSam
@Output(doc="sorted bam") var bam = outBam
@Output(doc="sorted bam index") var bamIndex = new File(outBam + "bai")
override def inputBams = List(sam)
@ -403,8 +403,8 @@ class dataProcessingV2 extends QScript {
@Output(doc="output sai file") var sai = outSai
def commandLine = bwaPath + " aln -q 5 " + reference + " -b " + bam + " > " + sai
this.isIntermediate = true
this.analysisName = queueLogDir + outBam + ".bwa_aln_se"
this.jobName = queueLogDir + outBam + ".bwa_aln_se"
this.analysisName = queueLogDir + outSai + ".bwa_aln_se"
this.jobName = queueLogDir + outSai + ".bwa_aln_se"
}
case class bwa_aln_pe1 (inBam: File, outSai1: File) extends CommandLineFunction {
@ -412,8 +412,8 @@ class dataProcessingV2 extends QScript {
@Output(doc="output sai file for 1st mating pair") var sai = outSai1
def commandLine = bwaPath + " aln -q 5 " + reference + " -b1 " + bam + " > " + sai
this.isIntermediate = true
this.analysisName = queueLogDir + outBam + ".bwa_aln_pe1"
this.jobName = queueLogDir + outBam + ".bwa_aln_pe1"
this.analysisName = queueLogDir + outSai1 + ".bwa_aln_pe1"
this.jobName = queueLogDir + outSai1 + ".bwa_aln_pe1"
}
case class bwa_aln_pe2 (inBam: File, outSai2: File) extends CommandLineFunction {
@ -421,8 +421,8 @@ class dataProcessingV2 extends QScript {
@Output(doc="output sai file for 2nd mating pair") var sai = outSai2
def commandLine = bwaPath + " aln -q 5 " + reference + " -b2 " + bam + " > " + sai
this.isIntermediate = true
this.analysisName = queueLogDir + outBam + ".bwa_aln_pe2"
this.jobName = queueLogDir + outBam + ".bwa_aln_pe2"
this.analysisName = queueLogDir + outSai2 + ".bwa_aln_pe2"
this.jobName = queueLogDir + outSai2 + ".bwa_aln_pe2"
}
case class bwa_sam_se (inBam: File, inSai: File, outBam: File, readGroup: String) extends CommandLineFunction {