223 lines
9.8 KiB
Scala
223 lines
9.8 KiB
Scala
/*
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* Copyright (c) 2011, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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import org.broadinstitute.sting.queue.QScript
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import org.broadinstitute.sting.queue.extensions.gatk._
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import collection.JavaConversions._
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import org.broadinstitute.sting.utils.interval.IntervalUtils
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class WholeGenomePipeline extends QScript {
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@Input(doc="Bam file list", shortName = "I", required=true)
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var bamList: File = _
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@Argument(doc="path to tmp space for storing intermediate bam files", shortName="cleanerTmpDir", required=true)
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var cleanerTmpDir: String = _
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@Argument(doc="Flag for running the whole genome (wg) or chromosome 20 (chr20). The default is chr20.", shortName="runType", required=false)
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var runType = "chr20"
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@Argument(doc="Chunk size. Defaults to 3,000,000", shortName="chunk", required=false)
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var chunkSize = 3000000
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val reference = "/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta"
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val dbsnp = "/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.vcf"
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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 omni = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/Omni25_sites_1525_samples.b37.vcf"
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trait CommandLineGATKArgs extends CommandLineGATK {
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this.reference_sequence = reference
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this.intervalsString = runIntervals
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this.memoryLimit = 2
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}
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case class ChrRange(chr: String, start: Long, stop: Long) {
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def toInterval = "%s:%d-%d".format(chr, start, stop)
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override def toString = toInterval
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}
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var runIntervals = List.empty[String]
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def script() {
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val rangeMap = Map(
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"cent1" -> new ChrRange("1", 121429168, 121529168),
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"cent16" -> new ChrRange("16", 40844464, 40944464),
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"chr20" -> new ChrRange("20", 1, 63025520),
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"chr20_100k" -> new ChrRange("20", 100001, 200000))
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var ranges = Traversable.empty[ChrRange]
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val chrs = IntervalUtils.getContigSizes(reference)
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runType = runType.toLowerCase
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if (runType == "wg") {
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// use all chromosomes from 1 to their length
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ranges = chrs.map { case (chr, len) => new ChrRange(chr, 1, len.longValue) }
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runIntervals = Nil
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} else {
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rangeMap.get(runType) match {
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case Some(range) =>
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ranges = List(range)
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runIntervals = List(range.toInterval)
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case None =>
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throw new RuntimeException("Inalid runType: " + runType + ". Must be one of: " + rangeMap.keys.mkString(", ") + ", or wg")
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}
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}
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val project = Array(".bams.list", ".bam.list", ".list").foldLeft(bamList.getName)(_.stripSuffix(_))
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val projectBase = project + "." + runType
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var chunkVcfs = List.empty[File]
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for (range <- ranges) {
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val chr = range.chr
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val chrStart = range.start
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val chrStop = range.stop
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var start = chrStart
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var chunkNumber = 1
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while (start <= chrStop) {
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val stop = (start + chunkSize - 1) min chrStop
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val chunkBase: String = "chunks/" + project + "." + runType + "_chunk_" + chr + "_" + chunkNumber
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val tmpBase: String = cleanerTmpDir + "/" + chunkBase
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val chunkInterval = "%s:%d-%d".format(chr, start, stop)
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val target = new RealignerTargetCreator with CommandLineGATKArgs
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target.intervalsString = List(chunkInterval)
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target.input_file :+= bamList
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target.mismatchFraction = 0.0
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target.maxIntervalSize = 700
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target.out = tmpBase + ".target.intervals"
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target.jobOutputFile = chunkBase + ".target.intervals.out"
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target.isIntermediate = true
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add(target)
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val clean = new IndelRealigner with CommandLineGATKArgs
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clean.intervalsString = List(chunkInterval)
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clean.input_file :+= bamList
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clean.targetIntervals = target.out
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clean.rodBind :+= RodBind("dbsnp", "VCF", dbsnp)
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clean.doNotUseSW = true
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clean.simplifyBAM = true
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clean.bam_compression = 1
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clean.out = tmpBase + ".cleaned.bam"
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clean.jobOutputFile = chunkBase + ".cleaned.bam.out"
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clean.jobPriority = 51
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clean.isIntermediate = true
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add(clean)
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val call = new UnifiedGenotyper with CommandLineGATKArgs
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call.intervalsString = List(chunkInterval)
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call.input_file :+= clean.out
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call.rodBind :+= RodBind("dbsnp", "VCF", dbsnp)
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call.downsample_to_coverage = 50
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call.standard_min_confidence_threshold_for_calling = 4.0
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call.standard_min_confidence_threshold_for_emitting = 4.0
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call.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY
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call.exactCalculation = org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel.ExactCalculation.LINEAR_EXPERIMENTAL
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call.genotype_likelihoods_model = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.BOTH
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call.GSA_PRODUCTION_ONLY = true
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call.out = chunkBase + ".vcf"
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call.jobOutputFile = call.out + ".out"
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call.jobPriority = 52
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add(call)
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chunkVcfs :+= call.out
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start += chunkSize
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chunkNumber += 1
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}
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}
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val combineVCFs = new CombineVariants with CommandLineGATKArgs
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combineVCFs.rodBind = chunkVcfs.zipWithIndex.map { case (vcf, index) => RodBind("input"+index, "VCF", vcf) }
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combineVCFs.rod_priority_list = chunkVcfs.zipWithIndex.map { case (vcf, index) => "input"+index }.mkString(",")
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combineVCFs.variantmergeoption = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION
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combineVCFs.genotypemergeoption = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.PRIORITIZE
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combineVCFs.out = projectBase + ".merged.vcf"
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combineVCFs.jobOutputFile = combineVCFs.out + ".out"
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combineVCFs.assumeIdenticalSamples = true
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add(combineVCFs)
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val sv = new SelectVariants with CommandLineGATKArgs
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sv.selectIndels = true
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sv.rodBind :+= RodBind("variant", "VCF", combineVCFs.out)
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sv.out = projectBase + ".indels.vcf"
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sv.jobOutputFile = sv.out + ".out"
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add(sv)
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val filter = new VariantFiltration with CommandLineGATKArgs
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filter.variantVCF = sv.out
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filter.filterName :+= "HARD_TO_VALIDATE"
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filter.filterExpression :+= "\"MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1\""
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filter.out = swapExt(sv.out, ".vcf", ".filtered.vcf")
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filter.jobOutputFile = filter.out + ".out"
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add(filter)
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val recombine = new CombineVariants with CommandLineGATKArgs
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recombine.rodBind :+= RodBind("indels", "VCF", sv.out)
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recombine.rodBind :+= RodBind("all", "VCF", combineVCFs.out)
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recombine.rod_priority_list = "indels,all"
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recombine.genotypemergeoption = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.PRIORITIZE
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recombine.out = swapExt(combineVCFs.out, ".vcf", ".filtered.vcf")
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recombine.jobOutputFile = recombine.out + ".out"
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add(recombine)
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val vr = new VariantRecalibrator with CommandLineGATKArgs
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vr.rodBind :+= RodBind("input", "VCF", recombine.out)
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vr.rodBind :+= RodBind("hapmap", "VCF", hapmap, "known=false,training=true,truth=true,prior=15.0")
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vr.rodBind :+= RodBind("omni", "VCF", omni, "known=false,training=true,truth=false,prior=12.0")
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vr.rodBind :+= RodBind("dbsnp", "VCF", dbsnp, "known=true,training=false,truth=false,prior=10.0")
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vr.use_annotation = List("QD", "SB", "HaplotypeScore", "HRun")
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vr.trustAllPolymorphic = true
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vr.TStranche = List("100.0", "99.9", "99.5", "99.3", "99.0", "98.9", "98.8", "98.5", "98.4", "98.3", "98.2", "98.1", "98.0", "97.9", "97.8", "97.5", "97.0", "95.0", "90.0")
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vr.tranches_file = swapExt(filter.out, ".vcf", ".tranches")
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vr.recal_file = swapExt(filter.out, ".vcf", ".recal")
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vr.jobOutputFile = vr.recal_file + ".out"
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add(vr)
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val ar = new ApplyRecalibration with CommandLineGATKArgs
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ar.rodBind :+= RodBind("input", "VCF", recombine.out)
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ar.tranches_file = vr.tranches_file
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ar.recal_file = vr.recal_file
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ar.ts_filter_level = 99.0
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ar.ignore_filter :+= "HARD_TO_VALIDATE"
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ar.out = swapExt(recombine.out, ".vcf", ".recalibrated.vcf")
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ar.jobOutputFile = ar.out + ".out"
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add(ar)
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val stdEval = new VariantEval with CommandLineGATKArgs
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stdEval.tranchesFile = vr.tranches_file
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stdEval.rodBind :+= RodBind("dbsnp", "VCF", dbsnp)
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stdEval.rodBind :+= RodBind("eval", "VCF", ar.out)
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stdEval.doNotUseAllStandardStratifications = true
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stdEval.doNotUseAllStandardModules = true
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stdEval.evalModule = List("SimpleMetricsByAC", "TiTvVariantEvaluator", "CountVariants")
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stdEval.stratificationModule = List("EvalRod", "CompRod", "Novelty", "Filter", "FunctionalClass", "Sample")
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stdEval.out = swapExt(ar.out, ".vcf", ".eval")
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stdEval.jobOutputFile = stdEval.out + ".out"
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add(stdEval)
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}
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}
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