136 lines
4.6 KiB
Scala
136 lines
4.6 KiB
Scala
package oneoffs.carneiro
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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 scala.io.Source._
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/**
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* Created by IntelliJ IDEA.
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* User: carneiro
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* Date: 3/17/11
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* Time: 11:29 AM
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* To change this template use File | Settings | File Templates.
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*/
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class downsampling extends QScript {
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@Input(doc="path to GenomeAnalysisTK.jar", shortName="gatk", required=true)
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var GATKjar: File = _
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@Input(doc="input BAM file - or list of BAM files", shortName="i", required=true)
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var input: File = _
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@Input(doc="target intervals", shortName="t", required=true)
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var targetIntervals: File = _
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@Input(doc="bootstrap number", shortName="b", required=false)
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var bootstrap: Int = 1
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@Input(doc="downsampling step", shortName="ds", required=true)
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var downsamplingStep: Double = _
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@Input(doc="downsampling floor", shortName="df", required=false)
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var downsamplingFloor: Double = 0.0
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@Input(doc="downsampling ceiling", shortName="dc", required=false)
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var downsamplingCeiling: Double = 1.0
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@Input(doc="Reference fasta file", shortName="R", required=false)
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var reference: File = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
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@Input(doc="dbSNP file", shortName="D", required=false)
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var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_132_b37.leftAligned.vcf")
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@Input(doc="project name", shortName="p", required=false)
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var base: String = "prj"
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def countLines(file: File):Int = {
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var count: Int = 0
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for (l <- fromFile(file).getLines) {
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count = count + 1
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}
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return count
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}
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val queueLogDir: String = ".qlog/"
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val outFile: String = "cov.out"
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val fullCoverageVCF = new File("/humgen/gsa-hpprojects/dev/carneiro/downsampling/analysis/fullcov/fullcov.F1.filtered.vcf")
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def script = {
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val nIntervals = math.min(200, countLines(targetIntervals))
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var f: Double = downsamplingCeiling
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var i: Int = 1
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while (f>=downsamplingFloor) {
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var b: Int = bootstrap
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while(b > 0) {
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val file = swapExt(outFile, ".out", ".F" + i + "." + b + ".out")
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add(cov(f, file))
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b = b - 1
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}
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val snp_out = new File(base + ".F" + i + ".raw.vcf")
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val filter_out = new File(base + ".F" + i + ".filtered.vcf")
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val eval_out = new File(base + ".F" + i + ".eval")
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add( snps(f, snp_out, nIntervals),
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filter(snp_out, filter_out),
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eval(filter_out, eval_out))
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f = f - downsamplingStep
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i = i + 1
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}
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}
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trait CommandLineGATKArgs extends CommandLineGATK {
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this.intervals :+= targetIntervals
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this.jarFile = GATKjar
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this.reference_sequence = reference
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this.memoryLimit = 4
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}
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case class cov (fraction: Double, outFile: File) extends Percent20xCoverage with CommandLineGATKArgs {
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this.input_file :+= input
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this.out = outFile
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this.ndrs = true
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this.downsample_to_fraction = fraction
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this.jobName = queueLogDir + outFile + ".cov"
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}
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case class snps (fraction: Double, outFile: File, nIntervals: Int) extends UnifiedGenotyper with CommandLineGATKArgs {
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this.memoryLimit = 6
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this.downsample_to_coverage = 600
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this.genotype_likelihoods_model = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.SNP
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this.input_file :+= input
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this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
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this.downsample_to_fraction = fraction
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this.scatterCount = nIntervals
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this.out = outFile
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this.analysisName = outFile + "_snps"
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this.jobName = queueLogDir + outFile
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}
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case class filter (inFile: File, outFile: File) extends VariantFiltration with CommandLineGATKArgs {
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this.filterName ++= List("SNPSBFilter","SNPQDFilter","SNPHRunFilter")
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this.filterExpression ++= List("\"SB>=0.10\"","\"QD<5.0\"","\"HRun>=4\"")
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this.clusterWindowSize = 10
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this.clusterSize = 3
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this.variantVCF = inFile
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this.out = outFile
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this.analysisName = outFile + "_filter"
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this.jobName = queueLogDir + outFile
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}
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case class eval (inFile: File, outFile: File) extends VariantEval with CommandLineGATKArgs {
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this.noST = true
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this.noEV = true
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this.evalModule ++= List("TiTvVariantEvaluator", "CountVariants", "ValidationReport")
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this.stratificationModule ++= List("EvalRod", "CompRod", "Novelty")
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this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
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this.rodBind :+= RodBind("eval", "VCF", inFile)
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this.rodBind :+= RodBind("comp", "VCF", fullCoverageVCF)
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this.out = outFile
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this.analysisName = outFile + "_VariantEval"
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this.jobName = queueLogDir + outFile
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}
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}
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