Expands targets by 50-bp on both sides when the expandIntervals argument is greater than 0.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5251 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran
parent
6d3b878dde
commit
c0a4af3809
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@ -1,4 +1,3 @@
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import org.broadinstitute.sting.commandline.ArgumentSource
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import org.broadinstitute.sting.datasources.pipeline.Pipeline
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import org.broadinstitute.sting.queue.extensions.gatk._
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@ -6,6 +5,7 @@ import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
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import org.broadinstitute.sting.queue.extensions.samtools._
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import org.broadinstitute.sting.queue.function.ListWriterFunction
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import org.broadinstitute.sting.queue.function.scattergather.{GatherFunction, CloneFunction, ScatterFunction}
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import org.broadinstitute.sting.queue.library.ipf.intervals.ExpandIntervals
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import org.broadinstitute.sting.queue.QScript
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import collection.JavaConversions._
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import org.broadinstitute.sting.utils.yaml.YamlUtils
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@ -16,42 +16,27 @@ class FullCallingPipeline extends QScript {
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@Argument(doc="the YAML file specifying inputs, interval lists, reference sequence, etc.", shortName="Y")
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var yamlFile: File = _
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@Input(doc="path to trigger track (for UnifiedGenotyper)", shortName="trigger", required=false)
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var trigger: File = _
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@Input(doc="path to refseqTable (for GenomicAnnotator) if not present in the YAML", shortName="refseqTable", required=false)
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var refseqTable: File = _
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@Input(doc="path to Picard FixMateInformation.jar. See http://picard.sourceforge.net/ .", required=false)
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@Input(doc="path to Picard FixMateInformation.jar. See http://picard.sourceforge.net/ .", shortName="P", required=false)
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var picardFixMatesJar: File = new java.io.File("/seq/software/picard/current/bin/FixMateInformation.jar")
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@Input(doc="path to GATK jar")
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@Input(doc="path to GATK jar", shortName="G")
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var gatkJar: File = _
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@Input(doc="per-sample downsampling level",shortName="dcov",required=false)
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var downsampling_coverage = 600
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@Input(doc="level of parallelism for IndelRealigner. By default is set to 1.", shortName="cleanerScatter", required=false)
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var num_cleaner_scatter_jobs = 1
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@Input(doc="level of parallelism for UnifiedGenotyper (both for Snps and Indels). By default is set to 20.", shortName="varScatter", required=false)
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@Input(doc="level of parallelism for UnifiedGenotyper (both for SNPs and indels). By default is set to 20.", shortName="varScatter", required=false)
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var num_var_scatter_jobs = 20
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@Argument(doc="expand each target in input intervals by the specified number of bases (50 bases by default)", shortName="expand", required=false)
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var expandIntervals = 50
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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=false)
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var tearScript: File = _
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// TODO: Fix command lines that pass -bigMemQueue
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@Argument(doc="Unused", shortName="bigMemQueue", required=false)
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var big_mem_queue: String = _
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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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trait CommandLineGATKArgs extends CommandLineGATK {
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@ -70,16 +55,10 @@ class FullCallingPipeline extends QScript {
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val projectBase: String = qscript.pipeline.getProject.getName
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if (qscript.refseqTable != null)
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qscript.pipeline.getProject.setRefseqTable(qscript.refseqTable)
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if (qscript.skip_cleaning) {
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endToEnd(projectBase + ".uncleaned", "recalibrated")
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} else {
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val recalibratedSamples = qscript.pipeline.getSamples.filter(_.getBamFiles.contains("recalibrated"))
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/
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for ( sample <- recalibratedSamples ) {
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val sampleId = sample.getId
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@ -166,140 +145,151 @@ class FullCallingPipeline extends QScript {
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samtoolsindex.jobOutputFile = new File(".queue/logs/Cleaning/%s/SamtoolsIndex.out".format(sampleId))
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samtoolsindex.bamFile = cleaned_bam
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samtoolsindex.analysisName = "index_cleaned_"+sampleId
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samtoolsindex.jobQueue = qscript.short_job_queue
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//samtoolsindex.jobQueue = qscript.short_job_queue
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add(samtoolsindex)
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}
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//endToEnd(projectBase + ".cleaned", "cleaned", adprRscript, seq, expKind)
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endToEnd(projectBase + ".cleaned", "cleaned")
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}
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}
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def endToEnd(base: String, bamType: String) = {
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val samples = qscript.pipeline.getSamples.filter(_.getBamFiles.contains(bamType)).toList
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val bamFiles = samples.map(_.getBamFiles.get(bamType))
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// step through the un-indel-cleaned graph:
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// 1a. call snps and indels
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val snps = new UnifiedGenotyper with CommandLineGATKArgs
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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.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.downsample_to_coverage = Some(qscript.downsampling_coverage)
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snps.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp)
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snps.memoryLimit = Some(6)
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val ei : ExpandIntervals = new ExpandIntervals(qscript.pipeline.getProject.getIntervalList, 1, qscript.expandIntervals, new File("Resources", base + ".flanks.interval_list"), qscript.pipeline.getProject.getReferenceFile, "INTERVALS", "INTERVALS")
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ei.jobOutputFile = new File(".queue/logs/Overall/ExpandIntervals.out")
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snps.scatterCount = qscript.num_var_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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trait ExpandedIntervals extends CommandLineGATK {
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if (qscript.expandIntervals > 0) {
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this.intervals :+= ei.outList
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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", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp)
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add(ei)
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}
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}
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// Call indels
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val indels = new UnifiedGenotyper with CommandLineGATKArgs with ExpandedIntervals
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indels.analysisName = base + "_indels"
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indels.jobOutputFile = new File(".queue/logs/IndelCalling/UnifiedGenotyper.indels.out")
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indels.memoryLimit = Some(6)
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indels.downsample_to_coverage = Some(600)
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indels.genotype_likelihoods_model = Option(org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.DINDEL)
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indels.input_file = bamFiles
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indels.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp)
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indels.out = new File("IndelCalls", base+".indels.vcf")
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indels.scatterCount = qscript.num_var_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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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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// Filter indels
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val filteredIndels = new VariantFiltration with CommandLineGATKArgs with ExpandedIntervals
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filteredIndels.analysisName = base + "_filteredIndels"
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filteredIndels.jobOutputFile = new File(".queue/logs/IndelCalling/VariantFiltration.indels.out")
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filteredIndels.filterName ++= List("IndelQUALFilter","IndelSBFilter","IndelQDFilter")
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filteredIndels.filterExpression ++= List("\"QUAL<30.0\"","\"SB>-1.0\"","\"QD<2\"")
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filteredIndels.variantVCF = indels.out
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filteredIndels.out = swapExt("IndelCalls", indels.out, ".vcf",".filtered.vcf")
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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.out = swapExt("SnpCalls",snps.out,".vcf",".annotated.vcf")
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// Call snps
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val snps = new UnifiedGenotyper with CommandLineGATKArgs with ExpandedIntervals
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snps.analysisName = base+"_snps"
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snps.jobOutputFile = new File(".queue/logs/SNPCalling/UnifiedGenotyper.snps.out")
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snps.memoryLimit = Some(6)
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snps.downsample_to_coverage = Some(600)
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snps.input_file = bamFiles
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snps.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getGenotypeDbsnpType, qscript.pipeline.getProject.getGenotypeDbsnp)
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snps.out = new File("SnpCalls", base+".snps.vcf")
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snps.scatterCount = qscript.num_var_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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// Filter snps
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val filteredSNPs = new VariantFiltration with CommandLineGATKArgs with ExpandedIntervals
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filteredSNPs.analysisName = base+"_filteredSNPs"
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filteredSNPs.jobOutputFile = new File(".queue/logs/SNPCalling/VariantFiltration.snps.out")
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filteredSNPs.filterName ++= List("SNPSBFilter","SNPQDFilter","SNPHRunFilter")
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filteredSNPs.filterExpression ++= List("\"SB>=0.10\"","\"QD<5.0\"","\"HRun>=4\"")
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filteredSNPs.clusterWindowSize = Some(10)
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filteredSNPs.clusterSize = Some(3)
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filteredSNPs.rodBind :+= RodBind("mask", "VCF", filteredIndels.out)
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filteredSNPs.variantVCF = snps.out
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filteredSNPs.out = swapExt("SnpCalls",snps.out,".vcf",".filtered.vcf")
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// Combine indels and snps into one VCF
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val combineAll = new CombineVariants with CommandLineGATKArgs with ExpandedIntervals
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combineAll.analysisName = base + "_combineAll"
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combineAll.jobOutputFile = new File(".queue/logs/Combined/CombineVariants.out")
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combineAll.variantMergeOptions = Option(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION)
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combineAll.rod_priority_list = "Indels,SNPs"
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combineAll.rodBind :+= RodBind("Indels", "VCF", filteredIndels.out)
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combineAll.rodBind :+= RodBind("SNPs", "VCF", filteredSNPs.out)
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combineAll.out = new File("CombinedCalls", base + ".allVariants.filtered.vcf")
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// Annotate variants
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val annotated = new GenomicAnnotator with CommandLineGATKArgs with ExpandedIntervals
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annotated.analysisName = base+"_annotated"
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annotated.jobOutputFile = new File(".queue/logs/Combined/GenomicAnnotator.out")
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annotated.rodToIntervalTrackName = "variant"
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annotated.analysisName = base+"_GenomicAnnotator"
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annotated.rodBind :+= RodBind("variant", "VCF", combineAll.out)
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annotated.rodBind :+= RodBind("refseq", "AnnotatorInputTable", qscript.pipeline.getProject.getRefseqTable)
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annotated.out = new File(base + ".snps_and_indels.filtered.annotated.vcf")
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//annotated.out = swapExt("VariantCalls", combineAll.out, ".vcf", ".annotated.vcf")
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// 2. hand filter with standard filter; mask indels; filter snp clusters
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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 = annotated.out
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handFilter.rodBind :+= RodBind("mask", "VCF", indels.out)
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handFilter.maskname = "IndelSite"
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handFilter.clusterWindowSize = Some(10)
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handfilter.clusterSize = Some(3)
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handFilter.filterName ++= List("StrandBias","QualByDepth","HomopolymerRun")
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handFilter.filterExpression ++= List("\"SB>=0.10\"","\"QD<5.0\"","\"HRun>=4\"")
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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. Variant eval the cut and the hand-filtered vcf files
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val smallEval = new VariantEval with CommandLineGATKArgs
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smallEval.jobOutputFile = new File(".queue/logs/SNPCalling/VariantEval.out")
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smallEval.rodBind :+= RodBind("eval", "VCF", handFilter.out)
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smallEval.evalModule ++= List("SimpleMetricsByAC", "TiTvVariantEvaluator", "CountVariants")
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smallEval.stratificationModule ++= List("EvalRod", "Novelty")
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smallEval.out = new File("SnpCalls", base+".gatkreport")
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// Variant eval the cut and the hand-filtered vcf files
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val smallEval = new VariantEval with CommandLineGATKArgs with ExpandedIntervals
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smallEval.analysisName = base+"_VariantEval"
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smallEval.jobOutputFile = new File(".queue/logs/Overall/VariantEval.out")
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smallEval.noST = true
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smallEval.noEV = true
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smallEval.evalModule ++= List("SimpleMetricsByAC", "TiTvVariantEvaluator", "CountVariants")
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smallEval.stratificationModule ++= List("EvalRod", "Novelty")
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smallEval.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getEvalDbsnpType, qscript.pipeline.getProject.getEvalDbsnp)
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smallEval.rodBind :+= RodBind("eval", "VCF", annotated.out)
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smallEval.out = swapExt(annotated.out, ".vcf", ".eval")
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//smallEval.out = new File("VariantCalls", base+".gatkreport")
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// 4. Combine indels and Snps into one VCF
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val combineAll = new CombineVariants with CommandLineGATKArgs
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combineAll.jobOutputFile = new File(".queue/logs/Overall/CombineVariants.out")
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combineAll.rod_priority_list = List("Indels", "SNPs")
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combineAll.rodBind :+= RodBind("SNPs", "VCF", handFilter.out)
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combineAll.rodBind :+= RodBind("Indels", "VCF", indels.out)
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combineAll.variantMergeOptions = Option(org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION)
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combineAll.analysisName = base + "_CombineCallsets"
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combineAll.out = new File(base + "allVariants.vcf")
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// 5. Make the bam list
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val listOfBams = new File(base +".BamFiles.list")
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// Make the bam list
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val listOfBams = new File("Resources", base +".BamFiles.list")
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val writeBamList = new ListWriterFunction
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writeBamList.analysisName = base + "_BamList"
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writeBamList.jobOutputFile = new File(".queue/logs/Overall/WriteBamList.out")
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writeBamList.inputFiles = bamFiles
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writeBamList.listFile = listOfBams
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writeBamList.analysisName = base + "_BamList"
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writeBamList.jobOutputFile = new File(".queue/logs/SNPCalling/bamlist.out")
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// 6. Run the ADPR and make pretty stuff
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add(indels, filteredIndels, snps, filteredSNPs, combineAll, annotated, smallEval, writeBamList)
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add(snps, indels, annotated,masker,handFilter,eval,writeBamList)
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if (qscript.tearScript != null){
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// Run the ADPR and make pretty stuff
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if (qscript.tearScript != null) {
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class rCommand extends CommandLineFunction{
|
||||
@Input(doc="R script")
|
||||
var script: File = _
|
||||
|
|
@ -315,20 +305,15 @@ class FullCallingPipeline extends QScript {
|
|||
}
|
||||
|
||||
val adpr = new rCommand
|
||||
adpr.analysisName = base + "_ADPR"
|
||||
adpr.bamlist = listOfBams
|
||||
adpr.yaml = qscript.yamlFile.getAbsoluteFile
|
||||
adpr.script = qscript.tearScript
|
||||
adpr.evalroot = eval.output
|
||||
adpr.jobOutputFile = new File(".queue/logs/SNPCalling/adpr.out")
|
||||
adpr.tearsheet = new File("SnpCalls", base + ".tearsheet.pdf")
|
||||
adpr.analysisName = base + "_ADPR"
|
||||
|
||||
adpr.evalroot = smallEval.out
|
||||
adpr.jobOutputFile = new File(".queue/logs/Overall/ADPR.out")
|
||||
adpr.tearsheet = new File("VariantCalls", base + ".tearsheet.pdf")
|
||||
|
||||
add(adpr)
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue