105 lines
4.6 KiB
Plaintext
Executable File
105 lines
4.6 KiB
Plaintext
Executable File
import org.broadinstitute.sting.commandline.Hidden
|
|
import org.broadinstitute.sting.gatk.walkers.genotyper.{GenotypeLikelihoodsCalculationModel, UnifiedGenotyperEngine}
|
|
import org.broadinstitute.sting.queue.extensions.gatk._
|
|
import org.broadinstitute.sting.queue.library.ipf.vcf.{VCFSimpleMerge, VCFExtractSites,VCFExtractIntervals}
|
|
import org.broadinstitute.sting.queue.{QException, QScript}
|
|
import collection.JavaConversions._
|
|
import org.broadinstitute.sting.utils.baq.BAQ
|
|
import org.broadinstitute.sting.utils.text.XReadLines
|
|
|
|
class batchMergePipeline extends QScript {
|
|
batchMerge =>
|
|
|
|
@Argument(doc="VCF list",shortName="vcfs") var vcfList: File = _
|
|
@Argument(doc="bam list",shortName="bams") var bamList: File = _
|
|
@Argument(doc="sting dir",shortName="sting") var stingDir: String = _
|
|
@Argument(doc="reference file",shortName="ref") var ref: File = _
|
|
@Argument(doc="batched output",shortName="batch") var batchOut: File = _
|
|
//@Argument(doc="read UG settings from header",shortName="ugh") var ugSettingsFromHeader : Boolean = false
|
|
@Hidden @Argument(doc="Min base q",shortName="mbq",required=false) var mbq : Int = 20
|
|
@Hidden @Argument(doc="Min map q",shortName="mmq",required=false) var mmq : Int = 20
|
|
@Hidden @Argument(doc="baq gap open penalty, using sets baq to calc when necessary",shortName="baqp",required=false) var baq : Int = -1
|
|
|
|
def script = {
|
|
|
|
var vcfs : List[File] = extractFileEntries(vcfList)
|
|
var bams : List[File] = extractFileEntries(bamList)
|
|
|
|
trait ExtractArgs extends VCFExtractSites {
|
|
this.keepFilters = false
|
|
this.keepInfo = false
|
|
this.keepQual = false
|
|
}
|
|
|
|
|
|
|
|
trait CombineVariantsArgs extends CombineVariants {
|
|
this.reference_sequence = batchMerge.ref
|
|
this.jarFile = new File(batchMerge.stingDir+"/dist/GenomeAnalysisTK.jar")
|
|
this.scatterCount = 10
|
|
this.memoryLimit=4
|
|
}
|
|
var combine : CombineVariants = new CombineVariants with CombineVariantsArgs
|
|
combine.out = swapExt(batchOut,".vcf",".variant.combined.vcf")
|
|
combine.rodBind ++= vcfs.map( u => new RodBind(u.getName,"vcf",u) )
|
|
|
|
add(combine)
|
|
|
|
var getVariantAlleles : List[VCFExtractSites] = vcfs.map( u => new VCFExtractSites(u, swapExt(batchOut.getParent,u,".vcf",".alleles.vcf")) with ExtractArgs)
|
|
var combineVCFs : VCFSimpleMerge = new VCFSimpleMerge
|
|
combineVCFs.vcfs = getVariantAlleles.map(u => u.outVCF)
|
|
combineVCFs.fai = new File(ref.getAbsolutePath+".fai")
|
|
combineVCFs.outVCF = swapExt(batchOut,".vcf",".pf.alleles.vcf")
|
|
var extractIntervals : VCFExtractIntervals = new VCFExtractIntervals(combine.out,swapExt(combine.out,".vcf",".intervals.list"),true)
|
|
//addAll(getVariantAlleles)
|
|
//add(combineVCFs,extractIntervals)
|
|
add(extractIntervals)
|
|
|
|
trait CalcLikelihoodArgs extends UGCalcLikelihoods {
|
|
this.reference_sequence = batchMerge.ref
|
|
this.min_base_quality_score = batchMerge.mbq
|
|
this.min_mapping_quality_score = batchMerge.mmq
|
|
if ( batchMerge.baq >= 0 ) {
|
|
this.baqGapOpenPenalty = batchMerge.baq
|
|
this.baq = BAQ.CalculationMode.CALCULATE_AS_NECESSARY
|
|
}
|
|
this.intervals :+= extractIntervals.listOut
|
|
this.allelesVCF = combine.out
|
|
this.jarFile = new File(stingDir+"/dist/GenomeAnalysisTK.jar")
|
|
this.memoryLimit = 4
|
|
this.scatterCount = 60
|
|
this.output_mode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES
|
|
this.genotyping_mode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES
|
|
}
|
|
|
|
def newUGCL( bams: (List[File],Int) ) : UGCalcLikelihoods = {
|
|
var ugcl = new UGCalcLikelihoods with CalcLikelihoodArgs
|
|
ugcl.input_file ++= bams._1
|
|
ugcl.out = new File("MBatch%d.likelihoods.vcf".format(bams._2))
|
|
return ugcl
|
|
}
|
|
|
|
var calcs: List[UGCalcLikelihoods] = bams.grouped(20).toList.zipWithIndex.map(u => newUGCL(u))
|
|
addAll(calcs)
|
|
|
|
trait CallVariantsArgs extends UGCallVariants {
|
|
this.reference_sequence = batchMerge.ref
|
|
this.intervals :+= extractIntervals.listOut
|
|
this.jarFile = new File(stingDir+"/dist/GenomeAnalysisTK.jar")
|
|
this.scatterCount = 30
|
|
this.memoryLimit = 8
|
|
this.output_mode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES
|
|
this.genotyping_mode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES
|
|
}
|
|
|
|
var cVars : UGCallVariants = new UGCallVariants with CallVariantsArgs
|
|
cVars.rodBind ++= calcs.map( a => new RodBind("variant"+a.out.getName.replace(".vcf",""),"vcf",a.out) )
|
|
cVars.out = batchOut
|
|
add(cVars)
|
|
}
|
|
|
|
override def extractFileEntries(in: File): List[File] = {
|
|
return (new XReadLines(in)).readLines.toList.map( new File(_) )
|
|
}
|
|
}
|