Script for calling indels in all phase 1 samples - VQSR part still needs work but raw calling is done
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5052 348d0f76-0448-11de-a6fe-93d51630548a
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delangel
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import net.sf.picard.reference.FastaSequenceFile
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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.gatk.DownsampleType
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import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel
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import org.broadinstitute.sting.queue.extensions.gatk._
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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.scattergather.{GatherFunction, CloneFunction, ScatterFunction}
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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 Phase1Calling extends QScript {
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qscript =>
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@Input(doc="path to GATK jar", shortName="gatk", required=true)
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var gatkJar: File = _
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@Input(doc="the chromosome to process", shortName="chr", required=false)
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var chr: Int = 20
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@Input(doc="output path", shortName="outputDir", required=false)
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var outputDir: String = "/humgen/1kg/processing/allPopulations_chr20_phase1_release/perPop.calls.indels"
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@Input(doc="base output filename", shortName="baseName", required=false)
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var baseName: String = ""
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@Input(doc="path to tmp space for storing intermediate bam files", shortName="outputTmpDir", required=false)
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var outputTmpDir: String = "/humgen/1kg/processing/allPopulations_chr20_phase1_release/perPop.cleaned.BAQed.bams"
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private val tmpDir: File = new File("/broad/shptmp/delangel/tmp/")
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private val reference: File = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
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private val dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_b37.rod")
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private val dbSNPIndels: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
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private val dindelPilotCalls: String = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg.pilot_release.merged.indels.sites.hg19.vcf"
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private val dindelAFRCalls: String = "/humgen/1kg/DCC/ftp/technical/working/20110111_august_dindel_indel_calls/AFR.dindel_august_release.20110110.sites.vcf.gz"
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private val dindelASNCalls: String = "/humgen/1kg/DCC/ftp/technical/working/20110111_august_dindel_indel_calls/ASN.dindel_august_release.20110110.sites.vcf.gz"
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private val dindelEURCalls: String = "/humgen/1kg/DCC/ftp/technical/working/20110111_august_dindel_indel_calls/EUR.dindel_august_release.20110110.sites.vcf.gz"
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private val dindelMask: String = "/humgen/1kg/processing/allPopulations_wholeGenome_august_release/pilot1.dindel.mask.bed"
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val hapmap = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf"
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val g1k = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg_pilot1_projectCalls/ALL.low_coverage.2010_07.hg19.vcf"
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val omni = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/764samples.deduped.b37.annot.vcf"
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val chromosomeLength = List(249250621,243199373,198022430,191154276,180915260,171115067,159138663,146364022,141213431,135534747,135006516,133851895,115169878,107349540,102531392,90354753,81195210,78077248,59128983,63025520,48129895,51304566)
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//val populations = List("ASW","CEU","CHB","CHS","CLM","FIN","GBR","JPT","LWK","MXL","PUR","TSI","YRI")
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//val populations = List("JPT","ASN","AMR")
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val populations = List("EUR","AMR","ASN","AFR")
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//val populations = List("FIN", "LWK")
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private val intervals: String = "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals"
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//val populations = List("ZZZ") // small set used for debugging
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private var pipeline: Pipeline = _
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trait CommandLineGATKArgs extends CommandLineGATK {
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this.jarFile = qscript.gatkJar
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this.reference_sequence = qscript.reference
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this.memoryLimit = Some(3)
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this.jobTempDir = qscript.tmpDir
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this.jobQueue = "gsa";
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//this.DBSNP = qscript.dbSNP
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}
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def script = {
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callThisChunk() // using scatter/gather capabilities of Queue so no need to for loop over 1Mb chunks of the chromosome
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}
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def callThisChunk() = {
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val interval = "%d".format(qscript.chr)
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for( population <- qscript.populations ) {
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val baseName: String = qscript.outputDir + "/" + population + ".indels.phase1.chr" + qscript.chr.toString
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var bamList: File = new File("/humgen/1kg/processing/allPopulations_chr20_phase1_release/perPop.cleaned.BAQed.bams/%s.phase1.chr%d.cleaned.bam".format(population, qscript.chr))
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if( population == "ASN" || population == "EUR" || population == "AFR" || population == "AMR" ) {
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bamList = new File("/humgen/1kg/processing/allPopulations_chr20_phase1_release/perPop.cleaned.BAQed.bams/%s.chr%d.cleaned.list".format(population, qscript.chr))
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}
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val rawCalls = new File(baseName + ".raw.vcf")
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val filteredCalls = new File(baseName + ".filtered.vcf")
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val clusterFile = new File(baseName + ".omni.clusters")
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val recalibratedCalls = new File(baseName + ".recal.vcf")
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val tranchesFile = new File(baseName + ".ts.omni.tranches")
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var call = new UnifiedGenotyper with CommandLineGATKArgs
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call.intervalsString ++= List(qscript.intervals)
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call.scatterCount = 63 // the smallest interval list has 63 intervals, one for each Mb on chr20
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call.setupScatterFunction = {
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case scatter: ScatterFunction =>
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scatter.commandDirectory = new File(qscript.outputDir+"IndelCalls/ScatterGather")
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scatter.jobOutputFile = new File(".queue/logs/IndelCalling/ScatterGather/Scatter.out")
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}
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call.setupCloneFunction = {
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case (clone: CloneFunction, index: Int) =>
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clone.commandDirectory = new File(qscript.outputDir+"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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call.setupGatherFunction = {
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case (gather: GatherFunction, source: ArgumentSource) =>
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gather.commandDirectory = new File(qscript.outputDir+"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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call.dcov = Some( 50 )
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call.stand_call_conf = Some( 4.0 )
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call.stand_emit_conf = Some( 4.0 )
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call.input_file :+= bamList
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call.out = rawCalls
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call.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF)
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call.analysisName = baseName + "_UG"
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call.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNPIndels)
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call.glm = Some(GenotypeLikelihoodsCalculationModel.Model.DINDEL)
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var filter = new VariantFiltration with CommandLineGATKArgs
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filter.intervalsString ++= List(qscript.intervals)
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filter.scatterCount = 10
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filter.variantVCF = rawCalls
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filter.out = filteredCalls
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filter.filterName ++= List("HARD_TO_VALIDATE")
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filter.filterExpression ++= List("\"MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1\"")
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filter.analysisName = baseName + "_VF"
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//filter.rodBind :+= RodBind("mask", "Bed", qscript.dindelMask)
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//filter.maskName = "InDel"
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var gvc = new GenerateVariantClusters with CommandLineGATKArgs
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//gvc.rodBind :+= RodBind("hapmap", "VCF", qscript.hapmap)
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gvc.rodBind :+= RodBind("1kg", "VCF", qscript.g1k)
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gvc.rodBind :+= RodBind("input", "VCF", filteredCalls )
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gvc.clusterFile = clusterFile
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gvc.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
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gvc.analysisName = baseName + "_GVC"
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gvc.intervalsString ++= List(qscript.intervals)
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//gvc.qual = Some(100) // clustering parameters to be updated soon pending new experimentation results
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//gvc.std = Some(4.5)
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//gvc.mG = Some(6)
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/*
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var vr = new VariantRecalibrator with CommandLineGATKArgs
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vr.rodBind :+= RodBind("1kg", "VCF", qscript.omni)
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vr.rodBind :+= RodBind("hapmap", "VCF", qscript.hapmap)
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vr.rodBind :+= RodBind("truthOmni", "VCF", qscript.omni)
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vr.rodBind :+= RodBind("truthHapMap", "VCF", qscript.hapmap)
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vr.rodBind :+= RodBind("input", "VCF", filteredCalls )
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vr.clusterFile = clusterFile
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vr.analysisName = baseName + "_VR"
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vr.intervalsString ++= List(qscript.intervals)
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vr.ignoreFilter ++= List("HARD_TO_VALIDATE")
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vr.target_titv = Some(2.3)
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vr.sm = Some(org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.SelectionMetricType.TRUTH_SENSITIVITY)
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vr.tranche ++= List("0.1", "1.0", "2.0", "3.0", "5.0", "10.0", "100.0")
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vr.out = recalibratedCalls
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vr.priorDBSNP = Some(10.0)
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vr.priorHapMap = Some(12.0)
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vr.prior1KG = Some(12.0)
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vr.tranchesFile = tranchesFile
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add(call, filter, gvc, vr) */
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add(call, filter)
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}
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}
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}
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