Using embedded GATK.
Hardcoded the reference and dbsnp since the training rods are also hardcoded, for now. Changed freeze/chr20 to wg/chr20/cent1 to also test the heaviest known shard. Other cleanup. TODO: Memory command line options or have the script figure it out using FLS or similar. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5799 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir
parent
03452c15c0
commit
08c13f3944
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/*
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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), chromosome 20 (chr20) or just the centromere of chromosome 1 (cent1). The default is cent1.", shortName="runType", required=false)
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var runType = "cent1"
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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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val chr1Centromere = new ChrRange("1", 121429168, 121529169)
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var runIntervals = List.empty[String]
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def script() {
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var ranges = Traversable.empty[ChrRange]
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val chrs = IntervalUtils.getContigSizes(reference)
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runType match {
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case "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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case "chr20" =>
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// use chromosome 20 from 1 to its length
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ranges = chrs.filterKeys(_ == "20").map { case (chr, len) => new ChrRange(chr, 1, len.longValue) }
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runIntervals = List(ranges.head.toInterval)
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case "cent1" =>
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// use chromosome 1 centromere
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ranges = List(chr1Centromere)
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runIntervals = List(ranges.head.toInterval)
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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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var interval = "%s:%d-%d".format(chr, start, stop)
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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 target = new RealignerTargetCreator with CommandLineGATKArgs
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target.intervalsString :+= interval
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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.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 :+= interval
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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 + ".clean.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 :+= interval
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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 = chunkBase + ".call.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 = projectBase + ".combine.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 = swapExt(combineVCFs.out, ".merged.vcf", ".indels.vcf")
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sv.jobOutputFile = swapExt(combineVCFs.jobOutputFile, ".combine.out", ".sv.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 = swapExt(sv.jobOutputFile, ".sv.out", ".filter.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 = swapExt(combineVCFs.jobOutputFile, ".combine.out", ".recombine.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, "training=true, prior=3.0")
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vr.rodBind :+= RodBind("1kg", "VCF", omni, "training=true, prior=3.0")
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vr.rodBind :+= RodBind("dbsnp", "VCF", dbsnp, "known=true")
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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("0.1","0.5","0.75","1.0","1.25","1.35","1.5","1.7","1.8","1.9","2.0","2.1","2.2","2.3","2.5","3.0","5.0","8.0","10.0")
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vr.tranches_file = swapExt(filter.out, ".merged.filtered.vcf", ".tranches")
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vr.recal_file = swapExt(filter.out, ".merged.filtered.vcf", "")
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vr.jobOutputFile = swapExt(combineVCFs.jobOutputFile, ".combine.out", ".cr.out")
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add(vr)
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val ar = new ApplyRecalibration with CommandLineGATKArgs
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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.ignore_filter :+= "HARD_TO_VALIDATE"
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ar.out = swapExt(filter.out, ".vcf", ".recalibrated.vcf")
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ar.jobOutputFile = swapExt(combineVCFs.jobOutputFile, ".combine.out", ".ar.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")
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stdEval.out = swapExt(ar.out, ".vcf", ".eval")
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stdEval.jobOutputFile = swapExt(combineVCFs.jobOutputFile, ".combine.out", ".eval.out")
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add(stdEval)
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}
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}
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@ -1,209 +0,0 @@
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import net.sf.picard.reference.FastaSequenceFile
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import org.broadinstitute.sting.datasources.pipeline.Pipeline
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import org.broadinstitute.sting.queue.extensions.gatk._
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import org.broadinstitute.sting.queue.extensions.samtools._
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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 WGSpipeline extends QScript {
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qscript =>
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@Input(doc="File with list of Bams", shortName = "bams", required = true)
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var bamList: File = _
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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="Project Name", shortName = "P", required = true)
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var project: String =_
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@Input(doc="path to tmp space for storing intermediate bam files", shortName="outputTmpDir", required=true)
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var outputTmpDir: String = _
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@Input(doc="reference file", shortName = "R", required = true)
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var reference: File = _
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@Input(doc="dbSNP", shortName = "D", required = true)
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var dbSNP: File = _
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@Input(doc="gsa-pipeline directory key", shortName = "dirKey", required = true)
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var dirkey: String =_
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@Input(doc="version id in format ### (ie 001)", shortName = "v", required = true)
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var version: String =_
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@Input(doc="Flag for running the entire genome. Otherwise a QC run of chr 20 is all that is run.", shortName = "freeze", required = false)
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var freeze: Boolean = false
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private 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 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/Omni25_sites_1525_samples.b37.vcf"
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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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}
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def script = {
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var chr: Int = 20
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var runType: String = "QC"
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if (qscript.freeze) {
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var chr: Int =20
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var runType = "freeze"
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} //TODO: Impliment whole genome once infrastructure for waiting for tmp space is available.
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// for now this will only run on chromosome 20 because otherwise we might run into space errors.
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else{
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var chr: Int = 20
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var runType = "QC"
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}
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val dirbase = qscript.dirkey + "/" + runType + "_v" +qscript.version
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val base = dirbase + "/Chunks/" + qscript.project + "." + runType
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val projectBase = dirbase + "/" + qscript.project + "." + runType
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val basesPerJob: Int = 3000000
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val lastBase: Int = 63025520
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var start: Int = 1
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var stop: Int = start - 1 + basesPerJob
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if( stop > lastBase ) { stop = lastBase }
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var jobNumber: Int = 1
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var mergeList: List[List[_]] = Nil
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while( jobNumber < (lastBase.toFloat / basesPerJob.toFloat) + 1.0) {
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var interval = "%d:%d-%d".format(chr, start, stop)
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val baseTmpName: String = qscript.outputTmpDir + "/" +base + "chunk_" +jobNumber
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val baseJobName: String = qscript.project + "_chunk_" + jobNumber
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// 1.) Create cleaning targets
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val target = new RealignerTargetCreator with CommandLineGATKArgs
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target.memoryLimit = Some(3)
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target.input_file :+= qscript.bamList
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target.intervalsString :+= interval
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target.out = new File(baseTmpName + ".target.intervals")
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target.mismatchFraction = Some(0.0)
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target.maxIntervalSize = Some(700)
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target.rodBind :+= RodBind("indels1", "VCF", qscript.dindelCalls)
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target.jobName = baseJobName + ".target"
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target.jobOutputFile = new File(baseTmpName + ".target.out")
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target.isIntermediate = true
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// 2.) Clean without SW
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val clean = new IndelRealigner with CommandLineGATKArgs
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val cleanedBam = new File(baseTmpName + ".cleaned.bam")
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clean.memoryLimit = Some(4)
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clean.input_file :+= qscript.bamList
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clean.intervalsString :+= interval
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clean.targetIntervals = target.out
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clean.jobOutputFile = new File (baseTmpName + ".clean.out" )
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clean.out = cleanedBam
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clean.doNotUseSW = true
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clean.simplifyBAM = true
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clean.rodBind :+= RodBind("indels1", "VCF", qscript.dindelCalls)
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clean.jobName = baseJobName + ".clean"
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clean.isIntermediate = true
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clean.compress = Some(0)
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clean.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNP )
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val call = new UnifiedGenotyper with CommandLineGATKArgs
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call.out = new File("/humgen/gsa-pipeline/"+base+ "chunk_" +jobNumber + ".vcf")
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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.baq = org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY
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call.jobName = baseJobName +".call"
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call.exactCalculation = org.broadinstitute.sting.gatk.walkers.genotyper.ExactAFCalculationModel.ExactCalculation.LINEAR_EXPERIMENTAL
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call.jobOutputFile = new File ("/humgen/gsa-pipeline/"+base+ "chunk_" +jobNumber + ".call.out" )
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call.input_file = List(clean.out)
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call.intervalsString :+= interval
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call.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNP )
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mergeList:+= List(baseJobName, call.out)
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add(target, clean, call)
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start += basesPerJob
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stop += basesPerJob
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if( stop > lastBase ) { stop = lastBase }
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jobNumber += 1
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}
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val combineVCFs = new CombineVariants with CommandLineGATKArgs
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combineVCFs.priority = ""
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for (c <- mergeList ){
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combineVCFs.rodBind :+= RodBind(c(0).toString, "VCF", c(1).toString)
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combineVCFs.priority += c(0).toString +","
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}
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combineVCFs.variantMergeOptions = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.VariantMergeType.UNION
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combineVCFs.jobName = qscript.project + ".combine"
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combineVCFs.out = new File("/humgen/gsa-pipeline/" + projectBase + ".merged.vcf")
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combineVCFs.jobOutputFile = new File ("/humgen/gsa-pipeline/" +projectBase + ".combine.out")
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combineVCFs.genotypemergeoption = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.PRIORITIZE
|
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combineVCFs.intervalsString :+= "20:1-63025520" ///TODO impliment only using the chr 20 or nothing if freeze
|
||||
combineVCFs.assumeIdenticalSamples = true
|
||||
|
||||
|
||||
val sv = new SelectVariants with CommandLineGATKArgs
|
||||
sv.selectIndels = true
|
||||
sv.out = swapExt(combineVCFs.out, "merged.vcf", "indelsOnly.vcf")
|
||||
sv.rodBind :+= RodBind("variant", "VCF", combineVCFs.out)
|
||||
sv.jobName = qscript.project + ".SV"
|
||||
sv.jobOutputFile = swapExt(combineVCFs.jobOutputFile, "combine.out", "sv.out")
|
||||
|
||||
val filter = new VariantFiltration with CommandLineGATKArgs
|
||||
filter.intervalsString :+= "20:1-63025520" ///TODO impliment only using the chr 20 or nothing if freeze
|
||||
filter.variantVCF = sv.out
|
||||
filter.out = swapExt(sv.out, ".vcf", ".filtered.vcf")
|
||||
filter.filterName ++= List("HARD_TO_VALIDATE") //ToDO check to make sure that this is what Guillermo recomends
|
||||
filter.filterExpression ++= List("\"MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1\"")
|
||||
filter.jobName = qscript.project + ".VF"
|
||||
filter.jobOutputFile = swapExt(sv.jobOutputFile, ".sv.out", ".filter.out")
|
||||
|
||||
|
||||
val recombine = new CombineVariants with CommandLineGATKArgs
|
||||
recombine.rodBind :+= RodBind("indels", "VCF", sv.out)
|
||||
recombine.rodBind :+= RodBind("all", "VCF", combineVCFs.out)
|
||||
recombine.priority = "indels,all"
|
||||
recombine.genotypemergeoption = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.PRIORITIZE
|
||||
recombine.out = swapExt(combineVCFs.out, "vcf", "filtered.vcf")
|
||||
recombine.jobName = qscript.project + ".recombine"
|
||||
recombine.jobOutputFile = swapExt(combineVCFs.jobOutputFile, "combine.out", "recombine.out")
|
||||
|
||||
val cr = new VariantRecalibrator with CommandLineGATKArgs
|
||||
cr.rodBind :+= RodBind("hapmap","VCF", qscript.hapmap, "training=true, prior=3.0")
|
||||
cr.rodBind :+= RodBind("1kg", "VCF", qscript.omni, "training=true, prior=3.0")
|
||||
cr.rodBind :+= RodBind("input", "VCF", recombine.out)
|
||||
cr.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNP, "known=true")
|
||||
cr.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
|
||||
cr.jobName = qscript.project + ".cr"
|
||||
cr.jobOutputFile = swapExt(combineVCFs.jobOutputFile, ".combine.out", ".cr.out")
|
||||
cr.intervalsString :+= "20" ///TODO impliment only using the chr 20 or nothing if freeze
|
||||
cr.allPoly = true
|
||||
cr.tranches_file =swapExt(filter.out, "merged.filtered.vcf", "tranches")
|
||||
cr.recal_file = swapExt(filter.out, "merged.filtered.vcf", "")
|
||||
cr.tranche ++= List("0.1","0.5","0.75","1.0","1.25","1.35","1.5","1.7","1.8","1.9","2.0","2.1","2.2","2.3","2.5","3.0","5.0","8.0","10.0")
|
||||
|
||||
val ar = new ApplyRecalibration with CommandLineGATKArgs
|
||||
ar.tranches_file = cr.tranches_file
|
||||
ar.recal_file = cr.recal_file
|
||||
ar.ignore_filter++= List("HARD_TO_VALIDATE")
|
||||
ar.out = swapExt(filter.out, "vcf", "recalibrated.vcf")
|
||||
ar.jobName = qscript.project + ".ar"
|
||||
ar.jobOutputFile = swapExt(combineVCFs.jobOutputFile, ".combine.out", ".ar.out")
|
||||
|
||||
val stdEval = new VariantEval with CommandLineGATKArgs
|
||||
stdEval.jobName = qscript.project+".eval"
|
||||
stdEval.jobOutputFile = swapExt(combineVCFs.jobOutputFile, ".combine.out", ".eval.out")
|
||||
stdEval.noST = true
|
||||
stdEval.noEV = true
|
||||
stdEval.evalModule ++= List("SimpleMetricsByAC", "TiTvVariantEvaluator", "CountVariants")
|
||||
stdEval.stratificationModule ++= List("EvalRod", "CompRod", "Novelty")
|
||||
stdEval.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNP)
|
||||
stdEval.rodBind :+= RodBind("eval", "VCF", ar.out)
|
||||
stdEval.out = swapExt(ar.out, ".vcf", ".eval")
|
||||
stdEval.tranchesFile = cr.tranches_file
|
||||
|
||||
add(combineVCFs, filter, sv, recombine, cr, ar, stdEval)
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue