120 lines
5.5 KiB
Plaintext
Executable File
120 lines
5.5 KiB
Plaintext
Executable File
import org.broadinstitute.sting.commandline.ArgumentCollection
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import org.broadinstitute.sting.queue.extensions.gatk._
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import org.broadinstitute.sting.queue.library.ipf.ExpandIntervals
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import org.broadinstitute.sting.queue.pipeline.PipelineArgumentCollection
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import org.broadinstitute.sting.queue.QScript
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import org.broadinstitute.sting.utils.text.XReadLines
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import collection.JavaConversions._
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class expanded_targets extends QScript {
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@ArgumentCollection var args : PipelineArgumentCollection = new PipelineArgumentCollection
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@Argument(shortName="bait",doc="The list of baits associated with the target list",required=false) var baitFile : File = _
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@Argument(shortName="thisTrigger",doc="The trigger track to use",required=false) var thisTrigger : File = new File("/humgen/gsa-hphome1/chartl/projects/exome/expanded/triggers/joined.omni.hiseq.vcf")
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def script = {
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// note : bam sorting and indexing handled outside of this script
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// GATK hacked by modifying GenomeLocSortedSet not to fuss about getting multiple instances of the same interval
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val intervalExpands : List[ExpandIntervals] = (new Range(0,40,1)).toList.map( u => {
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new ExpandIntervals(args.projectIntervals,1+5*u,5,new File("./"+args.projectName+"_expanded_%d_%d.interval_list".format(1+5*u,6+5*u)),args.projectRef,"TSV","INTERVALS")
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})
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trait GATKArgs extends CommandLineGATK {
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this.reference_sequence = args.projectRef
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this.DBSNP = args.projectDBSNP
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this.jarFile = args.gatkJar
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}
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val userDir = "."
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addAll(intervalExpands)
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val cleanIntervals : ExpandIntervals = new ExpandIntervals(args.projectIntervals,1,210,new File(userDir+"/"+args.projectName+"_expanded_full.interval_list"),args.projectRef,"TSV","INTERVALS")
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add(cleanIntervals)
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val uncleanBams : List[File] = asScalaIterable(new XReadLines(args.projectBams)).toList.map(u => new File(u))
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val realign : List[RealignerTargetCreator] = uncleanBams.map(u => {
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var rtc : RealignerTargetCreator = new RealignerTargetCreator with GATKArgs
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rtc.out = swapExt(userDir,u,".bam",".clean.targets.interval_list")
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rtc.input_file :+= u.getAbsoluteFile
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rtc.intervals :+= cleanIntervals.outList
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rtc.memoryLimit = Some(6)
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rtc
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})
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val clean : List[IndelRealigner] = realign.map( u => {
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var cleaner : IndelRealigner = new IndelRealigner with GATKArgs
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cleaner.targetIntervals = u.out
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cleaner.input_file = u.input_file
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cleaner.memoryLimit = Some(6)
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cleaner.out = new File(userDir+"/"+swapExt(u.out,".bam",".expanded.targets.bam").getName)
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cleaner.intervals :+= cleanIntervals.outList
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cleaner
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})
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addAll(realign)
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addAll(clean)
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val callFiles: List[File] = intervalExpands.map(u => makeCalls(u.outList,clean.map(h => swapExt(h.out,".bam",".sorted.bam"))))
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}
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def makeCalls(iList: File, bams: List[File]): File = {
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trait GATKArgs extends CommandLineGATK {
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this.reference_sequence = args.projectRef
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this.DBSNP = args.projectDBSNP
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this.jarFile = args.gatkJar
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this.intervals :+= iList
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}
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var call : UnifiedGenotyper = new UnifiedGenotyper with GATKArgs
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call.input_file = bams
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call.out = swapExt(iList,".interval_list",".raw.vcf")
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call.trig_emit_conf = Some(0.0)
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call.rodBind :+= new RodBind("trigger","vcf",thisTrigger)
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call.scatterCount = 10
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call.memoryLimit = Some(6)
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var filter : VariantFiltration = new VariantFiltration with GATKArgs
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filter.rodBind :+= new RodBind("variant","vcf",call.out)
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filter.filterExpression :+= "\"QD<5.0\""
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filter.filterName :+= "LowQualByDepth"
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filter.filterExpression :+= "\"SB>-0.10\""
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filter.filterName :+= "HighStrandBias"
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filter.out = swapExt(iList,".interval_list",".filtered.vcf")
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var callHiseq : UnifiedGenotyper = new UnifiedGenotyper with GATKArgs
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callHiseq.reference_sequence = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
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callHiseq.input_file = List(new File("/seq/picard_aggregation/EXT1/NA12878/v3/NA12878.bam"))
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callHiseq.rodBind :+= new RodBind("trigger","vcf",filter.out)
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callHiseq.out = swapExt(iList,".interval_list",".hiSeq.genotypes.vcf")
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callHiseq.trig_emit_conf = Some(0.0)
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callHiseq.scatterCount = 5
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add(call,filter,callHiseq)
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var eval : VariantEval = new VariantEval with GATKArgs
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eval.rodBind :+= new RodBind("evalInterval","vcf",filter.out)
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eval.rodBind :+= new RodBind("compHiSeq","vcf",new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/NA12878/NA12878.hg19.HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.vcf"))
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eval.rodBind :+= new RodBind("compHiSeq_atSites","vcf",callHiseq.out)
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eval.rodBind :+= new RodBind("compOMNI","vcf",new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/764samples.deduped.b37.annot.vcf"))
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eval.out = swapExt(iList,".interval_list",".eval")
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eval.reportType = Option(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.CSV)
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eval.memoryLimit = Some(4)
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add(eval)
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eval.out
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}
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class B37_to_HG19 extends CommandLineFunction {
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@Input(doc="vcf") var vcf : File = _
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@Output(doc="out") var outVCF : File = _
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def commandLine = "python /humgen/gsa-hphome1/chartl/sting/python/vcf_b36_to_hg18.py %s %s".format(vcf.getAbsolutePath,outVCF.getAbsolutePath)
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}
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class HG19_to_B37 extends B37_to_HG19 {
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override def commandLine = "python /humgen/gsa-hphome1/chartl/sting/python/vcf_b36_to_hg18.py -r %s %s".format(vcf.getAbsolutePath,outVCF.getAbsolutePath)
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}
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}
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