Includes UG version of indel genotyping rather than IGV2
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5191 348d0f76-0448-11de-a6fe-93d51630548a
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@ -44,7 +44,7 @@ class fullCallingPipeline extends QScript {
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@Input(doc="Skip indel-cleaning for BAM files (for testing only)", shortName="skipCleaning", required=false)
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var skip_cleaning = false
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@Input(doc="ADPR script", shortName ="tearScript", required=true)
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@Input(doc="ADPR script", shortName ="tearScript", required=false)
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var tearScript: File = _
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//@Input(doc="Sequencing maching name (for use by adpr)")
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@ -60,6 +60,8 @@ class fullCallingPipeline extends QScript {
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@Argument(doc="Job queue for short run jobs (<1hr)", shortName="shortJobQueue", required=false)
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var short_job_queue: String = _
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private var pipeline: Pipeline = _
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private var dbsnpType: String = _
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@ -208,92 +210,68 @@ class fullCallingPipeline extends QScript {
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snps.jobOutputFile = new File(".queue/logs/SNPCalling/UnifiedGenotyper.out")
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snps.analysisName = base+"_SNP_calls"
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snps.input_file = bamFiles
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//snps.annotation ++= List("AlleleBalance")
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snps.input_file = bamFiles
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snps.group :+= "Standard"
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snps.out = new File("SnpCalls", base+".vcf")
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//snps.standard_min_confidence_threshold_for_emitting = Some(10)
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//snps.min_mapping_quality_score = Some(20)
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//snps.min_base_quality_score = Some(20)
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snps.downsample_to_coverage = Some(qscript.downsampling_coverage)
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//snps.annotation :+= "QualByDepthV2"
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snps.rodBind :+= RodBind("dbsnp", dbsnpType, qscript.pipeline.getProject.getDbsnpFile)
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snps.memoryLimit = Some(6)
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//if (qscript.trigger != null) {
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// snps.trigger_min_confidence_threshold_for_calling = Some(30)
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// snps.rodBind :+= RodBind("trigger", "VCF", qscript.trigger)
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// // TODO: triggers need to get a name for comp-ing them if not dbSNP?
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// snps.rodBind :+= RodBind( "compTrigger", "VCF", qscript.trigger )
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//}
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// todo -- add generalize comp inputs
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//if ( qscript.comp1KGCEU != null ) {
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// snps.rodBind :+= RodBind( "comp1KG_CEU", "VCF", qscript.comp1KGCEU )
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//}
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snps.scatterCount = qscript.num_snp_scatter_jobs
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snps.setupScatterFunction = {
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case scatter: ScatterFunction =>
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scatter.commandDirectory = new File("SnpCalls/ScatterGather")
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scatter.jobOutputFile = new File(".queue/logs/SNPCalling/ScatterGather/Scatter.out")
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}
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snps.setupCloneFunction = {
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case (clone: CloneFunction, index: Int) =>
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clone.commandDirectory = new File("SnpCalls/ScatterGather/Scatter_%s".format(index))
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clone.jobOutputFile = new File(".queue/logs/SNPCalling/ScatterGather/Scatter_%s.out".format(index))
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}
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snps.setupGatherFunction = {
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case (gather: GatherFunction, source: ArgumentSource) =>
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gather.commandDirectory = new File("SnpCalls/ScatterGather/Gather_%s".format(source.field.getName))
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gather.jobOutputFile = new File(".queue/logs/SNPCalling/ScatterGather/Gather_%s.out".format(source.field.getName))
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}
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snps.setupScatterFunction = {
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case scatter: ScatterFunction =>
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scatter.commandDirectory = new File("SnpCalls/ScatterGather")
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scatter.jobOutputFile = new File(".queue/logs/SNPCalling/ScatterGather/Scatter.out")
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}
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snps.setupCloneFunction = {
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case (clone: CloneFunction, index: Int) =>
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clone.commandDirectory = new File("SnpCalls/ScatterGather/Scatter_%s".format(index))
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clone.jobOutputFile = new File(".queue/logs/SNPCalling/ScatterGather/Scatter_%s.out".format(index))
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}
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snps.setupGatherFunction = {
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case (gather: GatherFunction, source: ArgumentSource) =>
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gather.commandDirectory = new File("SnpCalls/ScatterGather/Gather_%s".format(source.field.getName))
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gather.jobOutputFile = new File(".queue/logs/SNPCalling/ScatterGather/Gather_%s.out".format(source.field.getName))
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}
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// indel genotyper does one sample at a time
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var indelCallFiles = List.empty[RodBind]
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var indelGenotypers = List.empty[IndelGenotyperV2 with CommandLineGATKArgs]
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var loopNo = 0
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var priority = ""
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for ( sample <- samples ) {
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val sampleId = sample.getId
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val bam = sample.getBamFiles.get(bamType)
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val indels = new UnifiedGenotyper with CommandLineGATKArgs
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indels.jobOutputFile = new File(".queue/logs/IndelCalling/UnifiedGenotyper.out")
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indels.analysisName = base+"_Indel_calls"
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indels.input_file = bamFiles
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indels.input_file = bamFiles
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indels.group :+= "Standard"
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indels.out = new File("IndelCalls", base+".vcf")
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indels.downsample_to_coverage = Some(qscript.downsampling_coverage)
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indels.rodBind :+= RodBind("dbsnp", dbsnpType, qscript.pipeline.getProject.getDbsnpFile)
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indels.memoryLimit = Some(6)
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indels.genotype_likelihoods_model = Option(org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.DINDEL)
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var indel = new IndelGenotyperV2 with CommandLineGATKArgs
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indel.jobOutputFile = new File(".queue/logs/IndelCalling/%s/IndelGenotyperV2.out".format(sampleId))
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indel.window_size = Some(350)
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indel.analysisName = "IndelGenotyper_"+sampleId
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indel.input_file :+= bam
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indel.out = swapExt("IndelCalls/IntermediateFiles/" + sampleId, bam,".bam",".indels.vcf")
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indel.downsample_to_coverage = Some(qscript.downsampling_coverage)
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indelCallFiles :+= RodBind("v"+loopNo.toString, "VCF", indel.out)
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//indel.scatterCount = qscript.num_indel_scatter_jobs
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indelGenotypers :+= indel
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if ( loopNo == 0 ) {
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priority = "v0"
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} else {
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priority += ",v"+loopNo.toString
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}
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loopNo += 1
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}
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val mergeIndels = new CombineVariants with CommandLineGATKArgs
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mergeIndels.jobOutputFile = new File(".queue/logs/IndelCalling/CombineVariants.out")
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mergeIndels.out = new TaggedFile("IndelCalls/" + qscript.pipeline.getProject.getName+".indels.vcf","vcf")
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mergeIndels.genotypemergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.UNSORTED)
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mergeIndels.priority = priority
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mergeIndels.variantmergeoption = Some(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION)
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mergeIndels.rodBind = indelCallFiles
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mergeIndels.analysisName = base+"_MergeIndels"
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mergeIndels.memoryLimit = Some(4)
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indels.scatterCount = qscript.num_snp_scatter_jobs
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indels.setupScatterFunction = {
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case scatter: ScatterFunction =>
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scatter.commandDirectory = new File("IndelCalls/ScatterGather")
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scatter.jobOutputFile = new File(".queue/logs/IndelCalling/ScatterGather/Scatter.out")
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}
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indels.setupCloneFunction = {
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case (clone: CloneFunction, index: Int) =>
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clone.commandDirectory = new File("IndelCalls/ScatterGather/Scatter_%s".format(index))
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clone.jobOutputFile = new File(".queue/logs/IndelCalling/ScatterGather/Scatter_%s.out".format(index))
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}
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indels.setupGatherFunction = {
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case (gather: GatherFunction, source: ArgumentSource) =>
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gather.commandDirectory = new File("IndelCalls/ScatterGather/Gather_%s".format(source.field.getName))
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gather.jobOutputFile = new File(".queue/logs/IndelCalling/ScatterGather/Gather_%s.out".format(source.field.getName))
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}
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// 1b. genomically annotate SNPs -- no longer slow
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val annotated = new GenomicAnnotator with CommandLineGATKArgs
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annotated.jobOutputFile = new File(".queue/logs/SNPCalling/GenomicAnnotator.out")
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annotated.rodBind :+= RodBind("variant", "VCF", snps.out)
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annotated.rodBind :+= RodBind("refseq", "AnnotatorInputTable", qscript.pipeline.getProject.getRefseqTable)
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//annotated.rodBind :+= RodBind("dbsnp", "AnnotatorInputTable", qscript.dbsnpTable)
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annotated.out = swapExt("SnpCalls",snps.out,".vcf",".annotated.vcf")
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//annotated.select :+= "dbsnp.name,dbsnp.refUCSC,dbsnp.strand,dbsnp.observed,dbsnp.avHet"
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annotated.rodToIntervalTrackName = "variant"
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annotated.analysisName = base+"_GenomicAnnotator"
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@ -301,7 +279,7 @@ class fullCallingPipeline extends QScript {
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val masker = new VariantFiltration with CommandLineGATKArgs
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masker.jobOutputFile = new File(".queue/logs/SNPCalling/Masker.out")
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masker.variantVCF = annotated.out
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masker.rodBind :+= RodBind("mask", "VCF", mergeIndels.out)
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masker.rodBind :+= RodBind("mask", "VCF", indels.out)
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masker.maskName = "NearIndel"
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masker.clusterWindowSize = Some(10)
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masker.clusterSize = Some(3)
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@ -312,7 +290,7 @@ class fullCallingPipeline extends QScript {
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val handFilter = new VariantFiltration with CommandLineGATKArgs
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handFilter.jobOutputFile = new File(".queue/logs/SNPCalling/HandFilter.out")
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handFilter.variantVCF = masker.out
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handFilter.rodBind :+= RodBind("mask", "VCF", mergeIndels.out)
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handFilter.rodBind :+= RodBind("mask", "VCF", indels.out)
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//handFilter.filterName ++= List("StrandBias","AlleleBalance","QualByDepth","HomopolymerRun")
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//handFilter.filterExpression ++= List("\"SB>=0.10\"","\"AB>=0.75\"","\"QD<5.0\"","\"HRun>=4\"")
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handFilter.filterName ++= List("StrandBias","QualByDepth","HomopolymerRun")
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@ -320,41 +298,6 @@ class fullCallingPipeline extends QScript {
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handFilter.out = swapExt("SnpCalls",annotated.out,".vcf",".handfiltered.vcf")
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handFilter.analysisName = base+"_HandFilter"
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// 3.i generate gaussian clusters on the masked vcf
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// todo -- args for annotations?
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// todo -- args for resources (properties file)
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// val clusters = new GenerateVariantClusters with CommandLineGATKArgs
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// clusters.jobOutputFile = new File(".queue/logs/SNPCalling/Clusters.out")
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// clusters.rodBind :+= RodBind("input", "VCF", masker.out)
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// clusters.rodBind :+= RodBind("dbsnp", "ROD", qscript.pipeline.getProject.getDbsnpFile)
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// val clusters_clusterFile = swapExt("SnpCalls/IntermediateFiles",snps.out,".vcf",".cluster")
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// clusters.clusterFile = clusters_clusterFile
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// clusters.memoryLimit = Some(4)
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// clusters.jobQueue = qscript.big_mem_queue
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// clusters.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
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// clusters.analysisName = base+"_Cluster"
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// 3.ii apply gaussian clusters to the masked vcf
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// val recalibrate = new VariantRecalibrator with CommandLineGATKArgs
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// recalibrate.jobOutputFile = new File(".queue/logs/SNPCalling/Recalibrator.out")
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// recalibrate.clusterFile = clusters.clusterFile
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// recalibrate.DBSNP = qscript.pipeline.getProject.getDbsnpFile
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// recalibrate.rodBind :+= RodBind("input", "VCF", masker.out)
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// recalibrate.out = swapExt("SnpCalls",masker.out,".vcf",".recalibrated.vcf")
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// recalibrate.target_titv = qscript.target_titv
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// recalibrate.tranches_file = swapExt("SnpCalls/IntermediateFiles", masker.out,".vcf",".recalibrate.tranches")
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// recalibrate.analysisName = base+"_VariantRecalibrator"
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// 3.iii apply variant cuts to the clusters
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// val cut = new ApplyVariantCuts with CommandLineGATKArgs
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// cut.jobOutputFile = new File(".queue/logs/SNPCalling/VariantCuts.out")
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// cut.rodBind :+= RodBind("input", "VCF", recalibrate.out)
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// cut.out = swapExt("SnpCalls",recalibrate.out,".vcf",".tranched.vcf")
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//cut.tranches_file = recalibrate.tranches_file
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// todo -- fdr inputs, etc
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// cut.fdr_filter_level = Some(1)
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// cut.analysisName = base+"_ApplyVariantCuts"
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// 4. Variant eval the cut and the hand-filtered vcf files
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val eval = new VariantEval with CommandLineGATKArgs
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@ -371,7 +314,6 @@ class fullCallingPipeline extends QScript {
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} else{
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eval.rodBind :+= RodBind("dbsnp", dbsnpType, qscript.pipeline.getProject.getDbsnpFile)
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}
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add(snps)
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// 5. Make the bam list
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val listOfBams = new File(base +".BamFiles.list")
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@ -384,35 +326,37 @@ class fullCallingPipeline extends QScript {
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// 6. Run the ADPR and make pretty stuff
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class rCommand extends CommandLineFunction{
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@Input(doc="R script")
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var script: File = _
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@Input(doc="pipeline yaml")
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var yaml: File = _
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@Input(doc="list of bams")
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var bamlist: File =_
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@Input(doc="Eval files root")
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var evalroot: File =_
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@Output(doc="tearsheet loc")
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var tearsheet: File =_
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def commandLine = "Rscript %s -yaml %s -bamlist %s -evalroot %s -tearout %s"
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.format(script, yaml, bamlist, evalroot, tearsheet)
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}
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add(snps, indels, annotated,masker,handFilter,eval,writeBamList)
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if (qscript.tearScript != null){
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class rCommand extends CommandLineFunction{
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@Input(doc="R script")
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var script: File = _
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@Input(doc="pipeline yaml")
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var yaml: File = _
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@Input(doc="list of bams")
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var bamlist: File =_
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@Input(doc="Eval files root")
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var evalroot: File =_
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@Output(doc="tearsheet loc")
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var tearsheet: File =_
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def commandLine = "Rscript %s -yaml %s -bamlist %s -evalroot %s -tearout %s".format(script, yaml, bamlist, evalroot, tearsheet)
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}
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val adpr = new rCommand
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val adpr = new rCommand
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adpr.bamlist = listOfBams
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adpr.yaml = qscript.yamlFile.getAbsoluteFile
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adpr.script = tearScript
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adpr.script = qscript.tearScript
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adpr.evalroot = eval.reportLocation
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adpr.jobOutputFile = new File(".queue/logs/SNPCalling/adpr.out")
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adpr.tearsheet = new File("SnpCalls", base + ".tearsheet.pdf")
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adpr.analysisName = base + "_ADPR"
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for ( igv2 <- indelGenotypers ) {
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add(igv2)
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add(adpr)
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}
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add(mergeIndels,annotated,masker,handFilter,eval,writeBamList,adpr)
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}
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}
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