Updates to calling pipeline
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3896 348d0f76-0448-11de-a6fe-93d51630548a
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chartl
parent
52f24c86fa
commit
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@ -1,3 +1,4 @@
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import org.broadinstitute.sting.queue.function.scattergather.{ContigScatterFunction, FixMatesGatherFunction}
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import org.broadinstitute.sting.queue.QScript._
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// Other imports can be added here
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@ -6,7 +7,7 @@ val unparsedArgs = setArgs(args)
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// very slow-to-run fast-to-write parse args function. Only worth changing if using lots of flags with lots of lookups.
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def parseArgs(flag: String): String = {
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val retNext: Boolean = false
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var retNext: Boolean = false
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for ( f <- unparsedArgs ) {
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if ( retNext ) {
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return f
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@ -38,11 +39,18 @@ class RealignerTargetCreator extends GatkFunction {
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class IndelRealigner extends GatkFunction {
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@Input(doc="Intervals to clean")
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var intervalsToClean: File = _
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@Input(doc="Number of contigs in the contig intervals",required=false)
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var numContigs: Int = 24
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@Scatter(classOf[ContigScatterFunction])
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@Input(doc="Contig intervals")
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var contigIntervals: File = _
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@Gather(classOf[FixMatesGatherFunction])
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@Output(doc="Cleaned bam file")
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var cleanedBam: File = _
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def commandLine = gatkCommandLine("IndelRealigner") + "--output %s -targetIntervals %s".format(cleanedBam,intervalsToClean)
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this.scatterCount = numContigs
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def commandLine = gatkCommandLine("IndelRealigner") + "--output %s -targetIntervals %s -L %s".format(cleanedBam,intervalsToClean,contigIntervals)
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}
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/////////////////////////////////////////////////
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@ -50,12 +58,31 @@ class IndelRealigner extends GatkFunction {
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/////////////////////////////////////////////////
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class UnifiedGenotyper extends GatkFunction {
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@Input(doc="An optional trigger track (trigger emit will be set to 0)",required=false)
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var trigger: File = _
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@Input(doc="A list of comparison files for annotation",required=false)
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var compTracks: List[(String,File)] = Nil
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@Input(doc="Calling confidence level (may change depending on depth and number of samples)")
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var callConf: Int = _
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@Gather(classOf[SimpleTextGatherFunction])
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@Output(doc="raw vcf")
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var rawVCF: File = _
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// todo -- add input for comps, triggers, etc
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def commandLine = gatkCommandLine("UnifiedGenotyper") + "-G Standard -A MyHaplotypeScore -varout %s".format(rawVCF)
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def commandLine = gatkCommandLine("UnifiedGenotyper") + "-G Standard -A MyHaplotypeScore -varout %s".format(rawVCF) +
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" -stand_emit_conf 10 -mmq 20 -mbq 20 -dt EXPERIMENTAL_BY_SAMPLE -dcov 200" +
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" -stand_call_conf %d".format(callConf) +
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( if (trigger == null ) "" else " -trig_call_conf %d -trig_emit_conf 0 -B trigger,VCF,%s".format(callConf,trigger) ) +
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makeCompString
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def makeCompString = {
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var S: String = ""
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for ( tup <- compTracks ) {
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S += " -B comp%s,VCF,%s".format(tup._1,tup._2)
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}
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S
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}
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}
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/////////////////////////////////////////////////
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@ -63,9 +90,9 @@ class UnifiedGenotyper extends GatkFunction {
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/////////////////////////////////////////////////
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class UnifiedGenotyperIndels extends GatkFunction {
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@Gather(classOf[SimpleTextGatherFunction])
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@Output(doc="indel vcf")
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var indelVCF: File = _
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@Gather(classOf[SimpleTextGatherFunction])
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// todo -- add inputs for the indel genotyper
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def commandLine = gatkCommandLine("UnifiedGenotyper") + "-varout %s -gm INDELS"
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@ -102,8 +129,15 @@ class GenerateVariantClusters extends GatkFunction {
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// todo -- args for annotations?
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// todo -- args for resources (properties file)
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def commandLine = gatkCommandLine("GenerateVariantClusters") + "-an QD -an SB -an MyHaplotypeScore -an HRun "
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+"-resources /humgen/gsa-scr1/chartl/sting/R -B input,VCF,%s -clusterFile %s".format(initialFilteredVCF,clusterFile)
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override def freeze = {
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// todo -- hacky change in memory limit -- fix this when more official roads to do this are in place
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this.memoryLimit = Some(8)
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this.jobQueue = "hugemem"
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super.freeze
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}
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def commandLine = gatkCommandLine("GenerateVariantClusters") + "-an QD -an SB -an MyHaplotypeScore -an HRun " +
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"-resources /humgen/gsa-scr1/chartl/sting/R -B input,VCF,%s -clusterFile %s".format(initialFilteredVCF,clusterFile)
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}
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/////////////////////////////////////////////////
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@ -118,8 +152,8 @@ class ApplyGaussianClusters extends GatkFunction {
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var recalibratedVCF: File = _
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// todo -- inputs for Ti/Tv expectation and other things
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def commandLine = gatkCommandLine("VariantRecalibrator") + "--target_titv 2.1 -resources /humgen/gsa-scr1/chartl/sting/R "
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+"-B input,VCF,%s -clusterFile %s -output %s".format(inputVCF,clusterFile,recalibratedVCF)
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def commandLine = gatkCommandLine("VariantRecalibrator") + "--target_titv 2.1 -resources /humgen/gsa-scr1/chartl/sting/R " +
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"-B input,VCF,%s -clusterFile %s -output %s".format(inputVCF,clusterFile,recalibratedVCF)
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}
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/////////////////////////////////////////////////
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@ -164,7 +198,7 @@ class VariantEval extends GatkFunction {
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var handFilteredVCF: File = _
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@Output(doc="An evaluation file")
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var evalOutput: File = _
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// todo -- input for additional comp tracks
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// todo -- make comp tracks command-line arguments or properties
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def commandLine = gatkCommandLine("VariantEval") + "-B evalOptimized,VCF,%s -B evalHandFiltered,VCF,%s -E CountFunctionalClasses -E CompOverlap -E CountVariants -E TiTvVariantEvaluator -o %s".format(optimizedVCF,handFilteredVCF,evalOutput)
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}
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@ -177,8 +211,8 @@ class VariantEval extends GatkFunction {
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val cleanSNPCalls = new UnifiedGenotyper
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val uncleanSNPCalls = new UnifiedGenotyper
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val cleanIndelCalls = new UnifiedGenotyper
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val uncleanIndelCalls = new UnifiedGenotyper
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val cleanIndelCalls = new UnifiedGenotyperIndels
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val uncleanIndelCalls = new UnifiedGenotyperIndels
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for ( bam <- inputs("bam") ) {
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@ -190,16 +224,19 @@ for ( bam <- inputs("bam") ) {
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// in advance, create the extension files
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val indel_targets = swapExt(bam,"bam","realigner_targets.interval_list")
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val cleaned_bam = swapExt(bam,"bam","cleaned.bam")
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val cleaned_bam = swapExt(bam,"bam","cleaned.bam") // note-- the scatter is in the definition itself
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// create the cleaning commands
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val targetCreator = new RealignerTargetCreator
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targetCreator.bamFiles += bam
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targetCreator.realignerTargets = indel_targets
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targetCreator.realignerIntervals = indel_targets
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val realigner = new IndelRealigner
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realigner.bamFiles = targetCreator.bamFiles
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realigner.contigIntervals = new File(parseArgs("-contigIntervals"))
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realigner.intervalsToClean = targetCreator.realignerIntervals
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realigner.numContigs = parseArgs("-numContigs").toInt
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realigner.cleanedBam = cleaned_bam
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// put clean bams in clean genotypers
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@ -216,48 +253,58 @@ val uncleanedBase: String = projectBase + ".uncleaned"
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def endToEnd(base: String, snps: UnifiedGenotyper, indels: UnifiedGenotyperIndels) = {
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// step through the un-indel-cleaned graph:
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// 1a. call snps and indels
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snps.rawVCF = base+".vcf"
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indels.rawVCF = base+".indels.vcf"
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// 1b. genomically annotate SNPs
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val annotated = new GenomicAnnotator
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annotated.inputVCF = snps.rawVCF
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annotated.annotatedVCF = swapExt(snps.rawVCF,".vcf",".annotated.vcf")
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// 2.a filter on cluster and near indels
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val masker = new VariantFiltration
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masker.unfilteredVCF = annotated.annotatedVCF
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masker.indelMask = indels.rawVCF
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masker.filteredVCF = swapExt(uncleanAnnotatedSNPCalls.annotatedVCF,".vcf",".indel.masked.vcf")
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// 2.b hand filter with standard filter
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val handFilter = new VariantFiltration
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handFilter.unfilteredVCF = annotated.annotatedVCF
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handFilter.indelMask = indels.rawVCF
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handFilter.filterNames = List("StrandBias","AlleleBalance","QualByDepth","HomopolymerRun")
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handFilter.filterExpressions = List("SB>=0.10","AB>=0.75","QD<5","HRun>=4")
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handFilter.filteredVCF = swapExt(annotated.annotatedVCF,".vcf",".handfiltered.vcf")
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// 3.i generate gaussian clusters on the masked vcf
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val clusters = new GenerateVariantClusters
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clusters.initialFilteredVCF = masker.filteredVCF
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clusters.clusterFile = swapExt(snps.rawVCF,".vcf",".cluster")
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// 3.ii apply gaussian clusters to the masked vcf
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val recalibrate = new ApplyGaussianClusters
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recalibrate.clusterFile = clusters.clusterFile
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recalibrate.inputVCF = masker.filteredVCF
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recalibrate.recalibratedVCF = swapExt(masker.filteredVCF,".vcf",".optimized.vcf")
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// 3.iii apply variant cuts to the clusters
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val cut = new ApplyVariantCuts
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cut.recalibratedVCF = recalibrate.recalibratedVCF
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cut.tranchedVCF = swapExt(recalibrate.recalibratedVCF,".vcf",".tranched.vcf")
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cut.tranchFile = swapExt(recalibrate.recalibratedVCF,".vcf",".tranch")
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// 4. Variant eval the cut and the hand-filtered vcf files
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val eval = new VariantEval
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eval.optimizedVCF = cut.tranchedVCF
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eval.handFilteredVCF = handFilter.filteredVCF
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eval.evalOutput = base+".eval"
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// step through the un-indel-cleaned graph:
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// 1a. call snps and indels
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snps.rawVCF = new File(base+".vcf")
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snps.callConf = 30
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snps.trigger = new File(parseArgs("-trigger"))
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// todo -- hack -- get this from the command line, or properties
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snps.compTracks :+= ( "comp1KG_CEU",new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg_pilot1_projectCalls/100328.CEU.hg18.sites.vcf") )
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snps.scatterCount = 100
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indels.indelVCF = new File(base+".indels.vcf")
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indels.scatterCount = 100
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// 1b. genomically annotate SNPs -- slow, but scatter it
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val annotated = new GenomicAnnotator
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annotated.inputVCF = snps.rawVCF
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annotated.annotatedVCF = swapExt(snps.rawVCF,".vcf",".annotated.vcf")
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annotated.scatterCount = 100
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// 2.a filter on cluster and near indels
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val masker = new VariantFiltration
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masker.unfilteredVCF = annotated.annotatedVCF
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masker.indelMask = indels.indelVCF
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masker.filteredVCF = swapExt(annotated.annotatedVCF,".vcf",".indel.masked.vcf")
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// 2.b hand filter with standard filter
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val handFilter = new VariantFiltration
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handFilter.unfilteredVCF = annotated.annotatedVCF
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handFilter.indelMask = indels.indelVCF
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handFilter.filterNames = List("StrandBias","AlleleBalance","QualByDepth","HomopolymerRun")
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handFilter.filterExpressions = List("SB>=0.10","AB>=0.75","QD<5","HRun>=4")
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handFilter.filteredVCF = swapExt(annotated.annotatedVCF,".vcf",".handfiltered.vcf")
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// 3.i generate gaussian clusters on the masked vcf
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val clusters = new GenerateVariantClusters
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clusters.initialFilteredVCF = masker.filteredVCF
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clusters.clusterFile = swapExt(snps.rawVCF,".vcf",".cluster")
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// 3.ii apply gaussian clusters to the masked vcf
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val recalibrate = new ApplyGaussianClusters
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recalibrate.clusterFile = clusters.clusterFile
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recalibrate.inputVCF = masker.filteredVCF
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recalibrate.recalibratedVCF = swapExt(masker.filteredVCF,".vcf",".optimized.vcf")
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// 3.iii apply variant cuts to the clusters
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val cut = new ApplyVariantCuts
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cut.recalibratedVCF = recalibrate.recalibratedVCF
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cut.tranchedVCF = swapExt(recalibrate.recalibratedVCF,".vcf",".tranched.vcf")
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cut.tranchFile = swapExt(recalibrate.recalibratedVCF,".vcf",".tranch")
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// 4. Variant eval the cut and the hand-filtered vcf files
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val eval = new VariantEval
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eval.optimizedVCF = cut.tranchedVCF
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eval.handFilteredVCF = handFilter.filteredVCF
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eval.evalOutput = new File(base+".eval")
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add(snps,indels,annotated,masker,handFilter,clusters,recalibrate,cut,eval)
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add(snps,indels,annotated,masker,handFilter,clusters,recalibrate,cut,eval)
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}
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endToEnd(uncleanedBase,uncleanSNPCalls,uncleanIndelCalls)
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endToEnd(cleanedBase,cleanSNPCalls,cleanIndelCalls)
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endToEnd(cleanedBase,cleanSNPCalls,cleanIndelCalls)
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setParams
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run
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@ -0,0 +1,21 @@
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package org.broadinstitute.sting.queue.function.scattergather
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import java.io.File
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import org.broadinstitute.sting.commandline.Input
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import org.broadinstitute.sting.queue.function.IntervalFunction
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class ContigScatterFunction extends ScatterFunction {
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type ScatterType = File
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@Input(doc="Reference file to scatter")
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var referenceFile: File = _
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override def setOriginalFunction(originalFunction: ScatterGatherableFunction) = {
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val command = originalFunction.asInstanceOf[IntervalFunction]
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referenceFile = command.referenceFile
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super.setOriginalFunction(originalFunction)
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}
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// TODO: Use the reference file for "all"
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def commandLine = "splitIntervalsByContig.py %s%s".format(originalInput, repeat(" ", scatterParts))
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}
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