import collection.SeqLike._ import management.CompilationMXBean import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.IndelStatistics import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk.RodBind._ import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction import org.broadinstitute.sting.queue.QScript import org.apache.commons.io.FilenameUtils import scala.Some ; class Phase1IndelVQSR extends QScript { qscript => // todo -- update to released version when things stabilize @Argument(shortName = "gatk",doc="gatkJarFile", required=false) var gatkJarFile: File = new File("/humgen/gsa-scr1/delangel/Sting_dev/dist/GenomeAnalysisTK.jar") @Argument(shortName = "R", doc="B37 reference sequence: defaults to broad standard location", required=false) var referenceFile: File = new File("/humgen/1kg/reference/human_g1k_v37.fasta") @Argument(shortName = "intervals", doc="intervals to evaluate. Only supports evaluation on chromosome 20 now, as most evaluation data is there", required=false) val TARGET_INTERVAL: String = "20" @Argument(shortName = "dataDir", doc="Path to the standard evaluation data files", required=false) val DATA_DIR = "/humgen/gsa-hpprojects/GATK/data/Comparisons/StandardForEvaluation/b37/" @Argument(shortName = "baseDir", doc="Path to the standard evaluation data files", required=false) val baseDir = "/humgen/gsa-scr1/delangel/VQSRIndels/data/" @Argument(shortName = "outDir", doc="Path to the output files", required=false) val OUT_DIR = "/humgen/gsa-scr1/delangel/VQSRIndels" @Argument(shortName = "truth", doc="VQSR truth file", required=false) var truthFile: File = new File("/humgen/gsa-scr1/delangel/devine_data/indel_hg19_051711_leftAligned_75percent_chr20.vcf" ) val populations = List("EUR","AMR","ASN","AFR") @Argument(shortName = "evalStandard1000GCalls", doc="If provided, we'll include some standard 1000G data for evaluation", required=false) val EVAL_STANDARD_1000G_CALLS: Boolean = true @Argument(shortName = "numG", doc="If provided, we'll include some standard 1000G data for evaluation", required=false) val numG: Int = 4 @Argument(shortName = "pctBad", doc="If provided, we'll include some standard 1000G data for evaluation", required=false) val pctBad: Double = 0.05 @Argument(shortName = "runName", doc="Run Name", required=false) val runName:String = "mills100" val COMPS_DIR = DATA_DIR + "comps/" val EVALS_DIR = DATA_DIR + "evals/" @Argument(shortName = "createAllPos", doc="If provided, create all POPS file", required=false) val CREATE_ALL_POPS_FILE: Boolean = false @Argument(shortName = "pops", doc="Populations to do", required=false) val moreIndelsToEval: List[String] = List("EUR","ASN","AFR","AMR") val VARIANT_TYPES: List[String] = List("indels", "snps") val VARIANT_TYPE_VT: Map[String, List[org.broad.tribble.util.variantcontext.VariantContext.Type]] = Map( "indels" -> List(org.broad.tribble.util.variantcontext.VariantContext.Type.INDEL, org.broad.tribble.util.variantcontext.VariantContext.Type.MIXED, org.broad.tribble.util.variantcontext.VariantContext.Type.NO_VARIATION), "snps" -> List(org.broad.tribble.util.variantcontext.VariantContext.Type.SNP, org.broad.tribble.util.variantcontext.VariantContext.Type.NO_VARIATION) ) val SITES_DIR: String = "sitesFiles" // path to b37 DBSNP val MY_DBSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_b37.leftAligned.vcf") var COMPS: List[Comp] = Nil def addComp(comp: Comp) { COMPS = comp :: COMPS } var EVALS: List[Eval] = Nil def addEval(eval: Eval) { EVALS = eval :: EVALS } def addEvalFromCMD(file: File, t: String) { addEval(new Eval(file.getName, t, file.getName)) } trait CommandLineGATKArgs extends CommandLineGATK { this.jarFile = qscript.gatkJarFile this.reference_sequence = qscript.referenceFile this.memoryLimit = Some(2) // this.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNP ) this.jobQueue = "week" this.intervalsString = List(TARGET_INTERVAL); } class Comp(val name: String, val evalType: String, val filename: String) { val file: File = new File(filename) } class Eval(val name: String, val evalType: String, val filename: String ) { val file: File = new File(filename) } def initializeStandardDataFiles() = { // // Standard evaluation files for indels // //addComp(new Comp("CG.38samples", "indels", COMPS_DIR+"CG.Indels.leftAligned.b37.vcf")) addComp(new Comp("g1k.pilot1.validation", "indels", COMPS_DIR+"pilot1_indel_validation_2009.b37.vcf")) //addComp(new Comp("NA12878.hand_curated", "indels", "NA12878.validated.curated.polymorphic.indels.vcf")) addComp(new Comp("NA12878.Mullikin", "indels", COMPS_DIR+"NA12878.DIPline.NQScm.expanded.chr20.b37.minReads_2_or_gt2bp.vcf")) addComp(new Comp("Mills.25pct", "indels", "/humgen/gsa-scr1/delangel/devine_data/indel_hg19_051711_leftAligned_25percent_chr20.vcf")) addComp(new Comp("Phase1Validation", "indels", "/humgen/gsa-scr1/delangel/VQSRIndels/1KG_Validation_Phase1_SNPs_05032011.HG19.finalized.vcf")) // // INDEL call sets // if ( EVAL_STANDARD_1000G_CALLS ) { // addEval(new Eval("dindel", "indels", "/humgen/gsa-scr1/delangel/officialCalls/20110201_chr20_phase1_indels/dindel/20110208.chr20.dindel2.ALL.sites.vcf")) addEval(new Eval("si", "indels", "/humgen/gsa-scr1/delangel/officialCalls/20101123.chr20.si.v2.combined.sites.leftAligned.vcf")) addEval(new Eval("bi", "indels", "/humgen/1kg/processing/official_release/phase1/ALL.wgs.broad.20101123.indels.sites.vcf")) addEval(new Eval("bc", "indels", "/humgen/gsa-scr1/delangel/officialCalls/20110201_chr20_phase1_indels/ALL.chr20.bc.20101123.indels.sites.leftAligned.vcf")) addEval(new Eval("ox", "indels", "/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.chr20.Oxford.20110407.indels.genotypes.sites.vcf")) addEval(new Eval("2of5", "indels", "/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.indels.2of5.chr20.vcf")) } // // Standard evaluation files for SNPs // /* addComp(new Comp("NA12878.homvar.GATK", "snps", "NA12878.HiSeq19.cut.vcf", true)) addComp(new Comp("CG.38samples", "snps", "CG.38samples.b37.vcf")) addComp(new Comp("NA12878.homvar.CG", "snps", "NA12878.CG.b37.snps.vcf", true)) addComp(new Comp("HapMap3.3", "snps", "hapmap3.3.sites_r27_nr.b37_fwd.vcf")) addComp(new Comp("OMNI.2.5M", "snps", "omni2.5.1212samples.b37.sites.chr20.monoAreAC0.vcf")) addComp(new Comp("g1k.pilot1.validation", "snps", "1000G.snp.validation.b37.vcf")) */ // // SNP call sets // } def script = { initializeStandardDataFiles(); // add additional files for evaluation, if necessary //moreSNPsToEval.foreach(addEvalFromCMD(_, "snps")) //moreIndelsToEval.foreach(addEvalFromCMD(_, "indels")) var ts:Double = 0.0 var tranches = List("99.9","99.0","98.0","97.0","95.0","92.0","90.0") var numG:Int = qscript.numG var pctBad:Double = qscript.pctBad val runName:String = qscript.runName + "_mG%d_pb%1.2f_QD_FS_HS_RP_IC".format(numG,pctBad) for( pop <- qscript.populations ) { val rawCalls = new File("/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110516Dev/calls/chr20/%s/%s.phase1.chr20.raw.indels.vcf".format(pop,pop)) //val filteredCalls = new File(baseName + ".v5."+runStr+".filtered.vcf") // val runname = //val clusterFile = new File(baseName + ".omni.clusters") //val recalibratedCalls = new File(baseName + ".recal.vcf") var tranchesFile = new File(qscript.baseDir +"%s_%s.tranches".format(pop,runName)) var recalFile = new File(qscript.baseDir +"%s_%s.recal".format(pop,runName)) var rscriptFile = new File(qscript.baseDir +"%s_%s.plots.R".format(pop,runName)) var vr = new VariantRecalibrator with CommandLineGATKArgs vr.rodBind :+= RodBind("input", "VCF",rawCalls ) vr.rodBind :+= RodBind("truth", "VCF",qscript.truthFile,"known=true,training=true,truth=true,prior=20.0" ) vr.mode = VariantRecalibratorArgumentCollection.Mode.INDEL vr.tranchesFile = tranchesFile vr.recalFile = recalFile vr.rscriptFile = rscriptFile vr.an = List("QD","FS","HaplotypeScore","ReadPosRankSum","InbreedingCoeff") vr.maxGaussians = Some(numG) vr.tranche = tranches vr.nt = Some(8) vr.percentBad = Some(pctBad) add(vr) for (tas: String <- tranches) { ts = tas.toDouble val outFile = new File("/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110516Dev/calls/chr20/%s/%s.phase1.chr20.recal_%s_ts_%4.1f.indels.sites.vcf".format(pop,pop,runName,ts)) var ar = new ApplyRecalibration with CommandLineGATKArgs ar.rodBind :+= RodBind("input", "VCF",rawCalls ) ar.mode = VariantRecalibratorArgumentCollection.Mode.INDEL ar.tranchesFile = tranchesFile ar.recalFile = recalFile ar.ts_filter_level = Some(ts) ar.sites_only = true ar.o = outFile add(ar) } } val VE = new MyEval() VE.VT = VARIANT_TYPE_VT("indels") VE.o = new File(OUT_DIR+"/"+ runName + ".eval") //VE.nt = Some(8) for (tas: String <- tranches) { ts = tas.toDouble var cm = new CombineVariants with CommandLineGATKArgs cm.o = new File("/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110516Dev/calls/chr20/ALL.phase1.chr20.recal_%s_ts_%4.1f.indels.sites.vcf".format(runName,ts)) for( pop <- qscript.populations ) { val outFile = new File("/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110516Dev/calls/chr20/%s/%s.phase1.chr20.recal_%s_ts_%4.1f.indels.sites.vcf".format(pop,pop,runName,ts)) cm.rodBind :+= RodBind(pop, "VCF", outFile) } add(cm) VE.rodBind :+= RodBind("eval_ts%4.1f".format(ts), "VCF", cm.o) } // add evals for ( calls <- EVALS ) VE.rodBind :+= RodBind("eval_" + calls.name, "VCF", calls.file) // add comps // VE.rodBind :+= RodBind("dbsnp", "VCF", MY_DBSNP) for ( comp <- COMPS ) VE.rodBind :+= RodBind("comp_" + comp.name, "VCF", comp.file) add(VE) } /** * Base class for VariantEval used here */ class MyEval() extends VariantEval with CommandLineGATKArgs { this.noST = true this.evalModule :+= "ValidationReport" //this.evalModule :+= "IndelMetricsByAC" this.evalModule :+= "IndelStatistics" this.evalModule :+= "CountVariants" //this.evalModule :+= "IndelClasses" } }