Intermediate commit of indel consensus VQSR script, a couple of new features added, not for general use
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5951 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel
parent
2c57721ed2
commit
78f5309656
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@ -30,8 +30,17 @@ class Phase1IndelVQSR extends QScript {
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@Argument(shortName = "outDir", doc="Path to the output files", required=false)
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val OUT_DIR = "/humgen/gsa-scr1/delangel/VQSRIndels"
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@Argument(shortName = "rawCalls", doc="VQSR raw input file", required=false)
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var rawCalls: File = new File("/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110525VQSRConsensus/calls/combined.phase1.chr20.raw.indels.vcf")
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@Argument(shortName = "truth", doc="VQSR truth file", required=false)
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var truthFile: File = new File("/humgen/gsa-scr1/delangel/devine_data/indel_hg19_051711_leftAligned_75percent_chr20.vcf" )
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@Argument(shortName = "training", doc="VQSR training file", required=false)
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var trainingFile: File = new File("/humgen/gsa-scr1/delangel/devine_data/indel_hg19_051711_leftAligned_75percent_chr20.vcf" )
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var noMultiallelicSites: Boolean = false;
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val populations = List("EUR","AMR","ASN","AFR")
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@Argument(shortName = "evalStandard1000GCalls", doc="If provided, we'll include some standard 1000G data for evaluation", required=false)
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@ -41,7 +50,7 @@ class Phase1IndelVQSR extends QScript {
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val numG: Int = 4
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@Argument(shortName = "pctBad", doc="If provided, we'll include some standard 1000G data for evaluation", required=false)
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val pctBad: Double = 0.05
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val pctBad: Double = 0.05
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@Argument(shortName = "runName", doc="Run Name", required=false)
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val runName:String = "mills100"
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@ -66,6 +75,14 @@ class Phase1IndelVQSR extends QScript {
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// path to b37 DBSNP
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val MY_DBSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_b37.leftAligned.vcf")
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val dindelCalls: String = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/AFR+EUR+ASN+1KG.dindel_august_release_merged_pilot1.20110126.sites.vcf"
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val DINDEL: String = "/humgen/gsa-scr1/delangel/officialCalls/20110201_chr20_phase1_indels/dindel/20110208.chr20.dindel2.ALL.sites.fixed.vcf"
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val SI: String = "/humgen/gsa-scr1/delangel/officialCalls/20101123.chr20.si.v2.combined.sites.leftAligned.vcf"
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val BI: String = "/humgen/1kg/processing/official_release/phase1/ALL.wgs.broad.20101123.indels.sites.vcf"
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val BC: String = "/humgen/gsa-scr1/delangel/officialCalls/20110201_chr20_phase1_indels/ALL.chr20.bc.20101123.indels.sites.leftAligned.vcf"
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val OX: String = "/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.chr20.Oxford.20110407.indels.genotypes.sites.vcf"
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var COMPS: List[Comp] = Nil
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def addComp(comp: Comp) { COMPS = comp :: COMPS }
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@ -79,7 +96,7 @@ class Phase1IndelVQSR extends QScript {
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this.reference_sequence = qscript.referenceFile
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this.memoryLimit = Some(2)
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// this.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNP )
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this.jobQueue = "week"
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this.jobQueue = "hour"
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this.intervalsString = List(TARGET_INTERVAL);
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}
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@ -100,7 +117,8 @@ class Phase1IndelVQSR extends QScript {
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//addComp(new Comp("NA12878.hand_curated", "indels", "NA12878.validated.curated.polymorphic.indels.vcf"))
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addComp(new Comp("NA12878.Mullikin", "indels", COMPS_DIR+"NA12878.DIPline.NQScm.expanded.chr20.b37.minReads_2_or_gt2bp.vcf"))
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addComp(new Comp("Mills.25pct", "indels", "/humgen/gsa-scr1/delangel/devine_data/indel_hg19_051711_leftAligned_25percent_chr20.vcf"))
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addComp(new Comp("Phase1Validation", "indels", "/humgen/gsa-scr1/delangel/VQSRIndels/1KG_Validation_Phase1_SNPs_05032011.HG19.finalized.vcf"))
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//addComp(new Comp("Phase1Validation", "indels", "/humgen/gsa-scr1/delangel/VQSRIndels/1KG_Validation_Phase1_SNPs_05032011.HG19.finalized.vcf"))
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addComp(new Comp("Phase1Validation", "indels", "/humgen/gsa-scr1/delangel/VQSRIndels/1000G.20101123.validation_set_v1.QCed.indels.vcf"))
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//
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@ -108,120 +126,117 @@ class Phase1IndelVQSR extends QScript {
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//
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if ( EVAL_STANDARD_1000G_CALLS ) {
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// addEval(new Eval("dindel", "indels", "/humgen/gsa-scr1/delangel/officialCalls/20110201_chr20_phase1_indels/dindel/20110208.chr20.dindel2.ALL.sites.vcf"))
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addEval(new Eval("si", "indels", "/humgen/gsa-scr1/delangel/officialCalls/20101123.chr20.si.v2.combined.sites.leftAligned.vcf"))
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addEval(new Eval("bi", "indels", "/humgen/1kg/processing/official_release/phase1/ALL.wgs.broad.20101123.indels.sites.vcf"))
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addEval(new Eval("bc", "indels", "/humgen/gsa-scr1/delangel/officialCalls/20110201_chr20_phase1_indels/ALL.chr20.bc.20101123.indels.sites.leftAligned.vcf"))
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addEval(new Eval("ox", "indels", "/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.chr20.Oxford.20110407.indels.genotypes.sites.vcf"))
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addEval(new Eval("dindel", "indels",qscript.DINDEL))
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addEval(new Eval("si", "indels",qscript.SI))
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addEval(new Eval("bi", "indels", qscript.BI))
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addEval(new Eval("bc", "indels", qscript.BC))
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addEval(new Eval("ox", "indels", qscript.OX))
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addEval(new Eval("2of5", "indels", "/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.indels.2of5.chr20.vcf"))
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}
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addEval(new Eval("2of5noMulti", "indels", "/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.indels.2of5.chr20.noMultiAllelic.vcf"))
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addEval(new Eval("union", "indels", "/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.indels.combined.chr20.vcf"))
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// addEval(new Eval("unionNoMulti", "indels", "/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.indels.combined.chr20.noMultiAllelic.vcf"))
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}
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//
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// Standard evaluation files for SNPs
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//
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/* addComp(new Comp("NA12878.homvar.GATK", "snps", "NA12878.HiSeq19.cut.vcf", true))
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addComp(new Comp("CG.38samples", "snps", "CG.38samples.b37.vcf"))
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addComp(new Comp("NA12878.homvar.CG", "snps", "NA12878.CG.b37.snps.vcf", true))
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addComp(new Comp("HapMap3.3", "snps", "hapmap3.3.sites_r27_nr.b37_fwd.vcf"))
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addComp(new Comp("OMNI.2.5M", "snps", "omni2.5.1212samples.b37.sites.chr20.monoAreAC0.vcf"))
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addComp(new Comp("g1k.pilot1.validation", "snps", "1000G.snp.validation.b37.vcf"))
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*/
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//
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// SNP call sets
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//
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}
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def script = {
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initializeStandardDataFiles();
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// add additional files for evaluation, if necessary
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//moreSNPsToEval.foreach(addEvalFromCMD(_, "snps"))
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//moreIndelsToEval.foreach(addEvalFromCMD(_, "indels"))
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var ts:Double = 0.0
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var tranches = List("99.9","99.0","98.0","97.0","95.0","92.0","90.0")
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var tranches = List("99.9","99.0","98.0","97.0","96.0","95.0","92.0","90.0","85.0","80.0","70.0")
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var numG:Int = qscript.numG
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var pctBad:Double = qscript.pctBad
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val runName:String = qscript.runName + "_mG%d_pb%1.2f_QD_FS_HS_RP_IC".format(numG,pctBad)
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for( pop <- qscript.populations ) {
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val rawCalls = new File("/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110516Dev/calls/chr20/%s/%s.phase1.chr20.raw.indels.vcf".format(pop,pop))
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//val filteredCalls = new File(baseName + ".v5."+runStr+".filtered.vcf")
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// val runname =
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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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var tranchesFile = new File(qscript.baseDir +"%s_%s.tranches".format(pop,runName))
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var recalFile = new File(qscript.baseDir +"%s_%s.recal".format(pop,runName))
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var rscriptFile = new File(qscript.baseDir +"%s_%s.plots.R".format(pop,runName))
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val rawCalls = qscript.rawCalls
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var tranchesFile = new File(qscript.baseDir +"%s.tranches".format(runName))
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var recalFile = new File(qscript.baseDir +"%s.recal".format(runName))
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var rscriptFile = new File(qscript.baseDir +"%s.plots.R".format(runName))
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var vr = new VariantRecalibrator with CommandLineGATKArgs
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vr.rodBind :+= RodBind("input", "VCF",rawCalls )
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vr.rodBind :+= RodBind("truth", "VCF",qscript.truthFile,"known=true,training=true,truth=true,prior=20.0" )
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vr.mode = VariantRecalibratorArgumentCollection.Mode.INDEL
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vr.tranchesFile = tranchesFile
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vr.recalFile = recalFile
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vr.rscriptFile = rscriptFile
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vr.an = List("QD","FS","HaplotypeScore","ReadPosRankSum","InbreedingCoeff")
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vr.maxGaussians = Some(numG)
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vr.tranche = tranches
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vr.nt = Some(8)
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vr.percentBad = Some(pctBad)
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add(vr)
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var vr = new VariantRecalibrator with CommandLineGATKArgs
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vr.rodBind :+= RodBind("input", "VCF",rawCalls )
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vr.rodBind :+= RodBind("truth", "VCF",qscript.truthFile,"known=true,training=false,truth=true,prior=15.0" )
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vr.rodBind :+= RodBind("training", "VCF",qscript.trainingFile,"known=true,training=true,truth=false,prior=12.0" )
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//vr.rodBind :+= RodBind("training2", "VCF",qscript.dindelCalls,"known=true,training=true,truth=false,prior=12.0" )
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vr.rodBind :+= RodBind("dbsnp", "VCF",qscript.MY_DBSNP,"known=true,training=false,truth=false,prior=8.0" )
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vr.rodBind :+= RodBind("BC", "VCF",qscript.BC,"consensus=true" )
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vr.rodBind :+= RodBind("BI", "VCF",qscript.BI,"consensus=true" )
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vr.rodBind :+= RodBind("SI", "VCF",qscript.SI,"consensus=true" )
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vr.rodBind :+= RodBind("DINDEL", "VCF",qscript.DINDEL,"consensus=true" )
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vr.rodBind :+= RodBind("OXFORD", "VCF",qscript.OX,"consensus=true" )
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for (tas: String <- tranches) {
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ts = tas.toDouble
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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))
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var ar = new ApplyRecalibration with CommandLineGATKArgs
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ar.rodBind :+= RodBind("input", "VCF",rawCalls )
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ar.mode = VariantRecalibratorArgumentCollection.Mode.INDEL
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ar.tranchesFile = tranchesFile
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ar.recalFile = recalFile
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ar.ts_filter_level = Some(ts)
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ar.sites_only = true
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ar.o = outFile
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add(ar)
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}
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}
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vr.mode = VariantRecalibratorArgumentCollection.Mode.INDEL
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vr.tranchesFile = tranchesFile
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vr.recalFile = recalFile
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vr.rscriptFile = rscriptFile
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// vr.an = List("QD","FS","HaplotypeScore","ReadPosRankSum","InbreedingCoeff","SB","")
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vr.an = List("QD","FS","HaplotypeScore","ReadPosRankSum","InbreedingCoeff")
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vr.maxGaussians = Some(numG)
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vr.tranche = tranches
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vr.nt = Some(8)
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vr.percentBad = Some(pctBad)
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vr.std = Some(12.0)
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//vr.ignore_filter = List("LowQual")
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add(vr)
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val VE = new MyEval()
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VE.VT = VARIANT_TYPE_VT("indels")
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VE.o = new File(OUT_DIR+"/"+ runName + ".eval")
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//VE.nt = Some(8)
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for (tas: String <- tranches) {
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ts = tas.toDouble
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var cm = new CombineVariants with CommandLineGATKArgs
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val outFile = new File("/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110603VQSRConsensus/calls/phase1.chr20.recal_%s_ts_%4.1f.indels.sites.vcf".format(runName,ts))
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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))
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for( pop <- qscript.populations ) {
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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))
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cm.rodBind :+= RodBind(pop, "VCF", outFile)
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}
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add(cm)
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var ar = new ApplyRecalibration with CommandLineGATKArgs
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ar.rodBind :+= RodBind("input", "VCF",rawCalls )
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ar.mode = VariantRecalibratorArgumentCollection.Mode.INDEL
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ar.tranchesFile = tranchesFile
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ar.recalFile = recalFile
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ar.ts_filter_level = Some(ts)
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ar.sites_only = true
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ar.o = outFile
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add(ar)
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VE.rodBind :+= RodBind("eval_ts%4.1f".format(ts), "VCF", cm.o)
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VE.rodBind :+= RodBind("eval_ts%4.1f".format(ts), "VCF", ar.o)
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}
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//VE.nt = Some(8)
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// add evals
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for ( calls <- EVALS )
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VE.rodBind :+= RodBind("eval_" + calls.name, "VCF", calls.file)
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// add comps
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// VE.rodBind :+= RodBind("dbsnp", "VCF", MY_DBSNP)
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// VE.rodBind :+= RodBind("dbsnp", "VCF", MY_DBSNP)
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for ( comp <- COMPS )
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VE.rodBind :+= RodBind("comp_" + comp.name, "VCF", comp.file)
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add(VE)
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}
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var ve2 = new MyEval
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for (tas: String <- tranches) {
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ts = tas.toDouble
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val outFile = new File("/humgen/gsa-hpprojects/dev/delangel/Phase1Calls/20110603VQSRConsensus/calls/phase1.chr20.recal_%s_ts_%4.1f.indels.sites.vcf".format(runName,ts))
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ve2.rodBind :+= RodBind("eval_ts%4.1f".format(ts), "VCF", outFile)
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}
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// comps are now other callsets to measure overlap
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ve2.rodBind :+= RodBind("comp_dindel", "VCF",qscript.DINDEL)
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ve2.rodBind :+= RodBind("comp_bc", "VCF", qscript.BC)
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ve2.rodBind :+= RodBind("comp_bi", "VCF", qscript.BI)
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ve2.rodBind :+= RodBind("comp_ox", "VCF", qscript.OX)
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ve2.rodBind :+= RodBind("comp_2of5", "VCF", "/humgen/gsa-scr1/delangel/otherIndelCallerAnalysis/ALL.indels.2of5.chr20.vcf")
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ve2.VT = VARIANT_TYPE_VT("indels")
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ve2.o = new File(OUT_DIR+"/"+ runName + ".comps.eval")
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add(ve2)
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}
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/**
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@ -229,10 +244,12 @@ class Phase1IndelVQSR extends QScript {
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*/
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class MyEval() extends VariantEval with CommandLineGATKArgs {
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this.noST = true
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this.nt = Some(8)
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this.evalModule :+= "ValidationReport"
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//this.evalModule :+= "IndelMetricsByAC"
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this.evalModule :+= "IndelStatistics"
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this.evalModule :+= "CountVariants"
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this.evalModule :+= "CompOverlap"
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//this.evalModule :+= "IndelClasses"
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}
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