Removed unnecessary dbSNP big-table dependency. Ti/Tv is now required. Consistent downsampling level for all programs. Spelling corrections. VariantEval now generates R-style output.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4355 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran
parent
145fb0df8b
commit
9820a12fa5
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@ -7,6 +7,7 @@ import org.broadinstitute.sting.queue.extensions.samtools._
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import org.broadinstitute.sting.queue.{QException, QScript}
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import collection.JavaConversions._
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import org.broadinstitute.sting.utils.yaml.YamlUtils
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import org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType
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class fullCallingPipeline extends QScript {
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qscript =>
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@ -29,33 +30,33 @@ class fullCallingPipeline extends QScript {
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@Input(doc="refseqTable", shortName="refseqTable")
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var refseqTable: File = _
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@Input(doc="dbsnpTable", shortName="dbsnpTable")
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var dbsnpTable: File = _
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@Input(doc="Picard FixMateInformation.jar. At the Broad this can be found at /seq/software/picard/current/bin/FixMateInformation.jar. Outside the broad see http://picard.sourceforge.net/")
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@Input(doc="Picard FixMateInformation.jar. At the Broad this can be found at /seq/software/picard/current/bin/FixMateInformation.jar. Outside the Broad see http://picard.sourceforge.net/")
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var picardFixMatesJar: File = _
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@Input(doc="gatk jar")
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var gatkJar: File = _
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@Input(doc="SNP cluster filter -- number SNPs",shortName="snpsInCluster",required=false)
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var snpsInCluster = 4
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var snpsInCluster = 3
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@Input(doc="SNP cluster filter -- window size",shortName="snpClusterWindow",required=false)
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var snpClusterWindow = 7
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var snpClusterWindow = 10
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@Input(doc="target titv for recalibration",shortName="titv",required=false)
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var target_titv = 2.1
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@Input(doc="target titv for recalibration",shortName="titv",required=true)
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var target_titv: Float = _
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@Input(doc="downsampling coverage",shortName="dcov",required=false)
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var downsampling_coverage = 200
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var downsampling_coverage = 300
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@Input(doc="Number of jobs to scatter unifeid genotyper",shortName="snpScatter",required=false)
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@Input(doc="Number of jobs to scatter UnifiedGenotyper",shortName="snpScatter",required=false)
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var num_snp_scatter_jobs = 50
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@Input(doc="Number of jobs to scatter indel genotyper",shortName="indelScatter",required=false)
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@Input(doc="Number of jobs to scatter IndelGenotyperV2",shortName="indelScatter",required=false)
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var num_indel_scatter_jobs = 5
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@Input(doc="Indel-clean BAM files",shortName="clean",required=false)
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var clean_bam_files = 1
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@Input(doc="ADPR script")
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var adprScript: File = _
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@ -71,11 +72,10 @@ class fullCallingPipeline extends QScript {
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this.intervals = qscript.pipeline.getProject.getIntervalList
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this.jarFile = qscript.gatkJar
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this.reference_sequence = qscript.pipeline.getProject.getReferenceFile
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this.memoryLimit = Some(2)
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}
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// ------------ SETUP THE PIPELINE ----------- //
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@ -84,27 +84,24 @@ class fullCallingPipeline extends QScript {
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val projectBase: String = qscript.pipeline.getProject.getName
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val cleanedBase: String = projectBase + ".cleaned"
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val uncleanedBase: String = projectBase + ".uncleaned"
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// there are commands that use all the bam files
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val recalibratedSamples = qscript.pipeline.getSamples
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.filter(_.getBamFiles.contains("recalibrated"))
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val recalibratedSamples = qscript.pipeline.getSamples.filter(_.getBamFiles.contains("recalibrated"))
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val adprRScript = qscript.adprScript
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val seq = qscript.machine
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val expKind = qscript.protocol
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for ( sample <- recalibratedSamples ) {
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// put unclean bams in unclean genotypers
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// in advance, create the extension files
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// put unclean bams in unclean genotypers in advance, create the extension files
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val bam = sample.getBamFiles.get("recalibrated")
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if (!sample.getBamFiles.contains("cleaned"))
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if (!sample.getBamFiles.contains("cleaned")) {
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sample.getBamFiles.put("cleaned", swapExt(bam,"bam","cleaned.bam"))
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val cleaned_bam = sample.getBamFiles.get("cleaned")
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}
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val cleaned_bam = sample.getBamFiles.get("cleaned")
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val indel_targets = swapExt(bam,"bam","realigner_targets.interval_list")
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// create the cleaning commands
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val targetCreator = new RealignerTargetCreator with CommandLineGATKArgs
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targetCreator.analysisName = "CreateTargets_"+bam.getName
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targetCreator.input_file :+= bam
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@ -126,8 +123,6 @@ class fullCallingPipeline extends QScript {
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def outputBam = fixed
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}
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// realigner.out = cleaned_bam
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// realigner.scatterClass = classOf[ContigScatterFunction]
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// realigner.setupGatherFunction = { case (f: BamGatherFunction, _) => f.jarFile = qscript.picardFixMatesJar }
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@ -163,27 +158,33 @@ class fullCallingPipeline extends QScript {
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samtoolsindex.analysisName = "index_"+cleaned_bam.getName
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// COMMENT THIS NEXT BLOCK TO SKIP CLEANING
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if ( realigner.scatterCount > 1 )
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add(targetCreator,realigner,samtoolsindex)
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else
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add(targetCreator,realigner,fixMates,samtoolsindex)
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if (qscript.clean_bam_files == 1) {
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if ( realigner.scatterCount > 1 ) {
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add(targetCreator,realigner,samtoolsindex)
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} else {
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add(targetCreator,realigner,fixMates,samtoolsindex)
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}
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}
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}
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val recalibratedBamFiles = recalibratedSamples
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.map(_.getBamFiles.get("recalibrated"))
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.toList
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val cleanBamFiles = qscript.pipeline.getSamples
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.filter(_.getBamFiles.contains("cleaned"))
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.map(_.getBamFiles.get("cleaned"))
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.toList
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// actually make calls
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//endToEnd(uncleanedBase,recalibratedBamFiles, adprRscript, seq, expKind)
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endToEnd(uncleanedBase,recalibratedBamFiles, seq, expKind)
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// COMMENT THIS NEXT LINE TO AVOID CALLING ON CLEANED FILES
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//endToEnd(cleanedBase,cleanBamFiles, adprRscript, seq, expKind)
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endToEnd(cleanedBase,cleanBamFiles, seq, expKind)
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if (qscript.clean_bam_files == 1) {
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// COMMENT THIS NEXT LINE TO AVOID CALLING ON CLEANED FILES
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//endToEnd(cleanedBase, cleanBamFiles, adprRscript, seq, expKind)
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endToEnd(cleanedBase, cleanBamFiles, seq, expKind)
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} else {
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//endToEnd(uncleanedBase, recalibratedBamFiles, adprRscript, seq, expKind)
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endToEnd(uncleanedBase, recalibratedBamFiles, seq, expKind)
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}
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}
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//def endToEnd(base: String, bamFiles: List[File], adprthing: File, seqinfo: String, exptype: String) = {
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@ -199,7 +200,7 @@ class fullCallingPipeline extends QScript {
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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(200)
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snps.downsample_to_coverage = Some(qscript.downsampling_coverage)
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//snps.annotation :+= "QualByDepthV2"
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if (qscript.trigger != null) {
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@ -216,7 +217,6 @@ class fullCallingPipeline extends QScript {
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snps.scatterCount = qscript.num_snp_scatter_jobs
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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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@ -227,9 +227,9 @@ class fullCallingPipeline extends QScript {
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indel.analysisName = "IndelGenotyper_"+bam.getName
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indel.input_file :+= bam
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indel.out = swapExt(bam,".bam",".indels.vcf")
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indel.downsample_to_coverage = Some(500)
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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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//indel.scatterCount = qscript.num_indel_scatter_jobs
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indelGenotypers :+= indel
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@ -248,21 +248,19 @@ class fullCallingPipeline extends QScript {
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mergeIndels.rodBind = indelCallFiles
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mergeIndels.analysisName = base+"_MergeIndels"
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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.rodBind :+= RodBind("variant", "VCF", snps.out)
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annotated.rodBind :+= RodBind("refseq", "AnnotatorInputTable", qscript.refseqTable)
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annotated.rodBind :+= RodBind("dbsnp", "AnnotatorInputTable", qscript.dbsnpTable)
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//annotated.rodBind :+= RodBind("dbsnp", "AnnotatorInputTable", qscript.dbsnpTable)
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annotated.out = swapExt(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.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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// 2.a filter on cluster and near indels
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val masker = new VariantFiltration with CommandLineGATKArgs
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masker.variantVCF = annotated.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.maskName = "NearIndel"
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masker.clusterWindowSize = Some(qscript.snpClusterWindow)
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@ -270,7 +268,6 @@ class fullCallingPipeline extends QScript {
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masker.out = swapExt(annotated.out,".vcf",".indel.masked.vcf")
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masker.analysisName = base+"_Cluster_and_Indel_filter"
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// 2.b hand filter with standard filter
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val handFilter = new VariantFiltration with CommandLineGATKArgs
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handFilter.variantVCF = masker.out
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@ -280,7 +277,6 @@ class fullCallingPipeline extends QScript {
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handFilter.out = swapExt(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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@ -295,7 +291,6 @@ class fullCallingPipeline extends QScript {
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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.clusterFile = clusters.clusterFile
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@ -316,14 +311,13 @@ class fullCallingPipeline extends QScript {
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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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eval.rodBind :+= RodBind("evalOptimized", "VCF", cut.out)
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eval.rodBind :+= RodBind("evalHandFiltered", "VCF", handFilter.out)
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eval.evalModule ++= List("CountFunctionalClasses", "CompOverlap", "CountVariants", "TiTvVariantEvaluator")
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//eval.reportLocation = new File(base+".eval")
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//eval.reportType = "R"
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eval.reportLocation = new File(base+".eval")
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eval.reportType = Option(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.R)
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eval.analysisName = base+"_VariantEval"
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add(snps)
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@ -353,14 +347,11 @@ class fullCallingPipeline extends QScript {
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// to be in the working directory. When database access is ready, this and the protocol and sequencer parameters of
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//the r script will go away.
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for ( igv2 <- indelGenotypers ) {
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add(igv2)
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}
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// add(mergeIndels,annotated,masker,handFilter,clusters,recalibrate,cut,eval,adpr)
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add(mergeIndels,annotated,masker,handFilter,clusters,recalibrate,cut,eval)
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}
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}
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