81 lines
2.9 KiB
Scala
Executable File
81 lines
2.9 KiB
Scala
Executable File
package oneoffs.depristo
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import org.broadinstitute.sting.queue.QScript
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import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction
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import org.broadinstitute.sting.queue.extensions.gatk._
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import org.broadinstitute.sting.queue.function.JavaCommandLineFunction
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class ExomePostQCEval extends QScript {
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@Argument(doc="gatkJarFile", required=false)
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var gatkJarFile: File = new File("/home/radon01/depristo/dev/GenomeAnalysisTK/trunk/dist/GenomeAnalysisTK.jar")
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@Argument(shortName = "R", doc="ref", required=false)
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var referenceFile: File = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
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// todo -- should accept argument list as well
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@Argument(shortName = "eval", doc="VCFs to evaluate", required=true)
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var evalVCFs: List[File]= _
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@Argument(shortName = "intervals", doc="intervals", required=true)
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val myIntervals: String = null;
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@Argument(shortName = "RPath", doc="RPath", required=false)
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var RPath: File = new File("../R")
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@Argument(shortName = "dbSNP", doc="dbSNP", required=false)
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val dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/bundle/current/b37/dbsnp_132.b37.vcf")
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trait UNIVERSAL_GATK_ARGS extends CommandLineGATK {
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this.logging_level = "INFO";
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this.jarFile = gatkJarFile;
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this.reference_sequence = referenceFile;
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this.memoryLimit = 4
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}
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// TODO -- should include "standard" eval for plotting expectations
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def script = {
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for ( evalVCF <- evalVCFs ) {
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// The basic summary eval
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createEval(evalVCF, ".summary",
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List("TiTvVariantEvaluator", "CountVariants", "CompOverlap"),
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List("FunctionalClass"))
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// The basic summary eval, by AF
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createEval(evalVCF, ".byAC",
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List("TiTvVariantEvaluator", "CountVariants", "CompOverlap"),
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List("AlleleCount"))
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// By sample
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createEval(evalVCF, ".bySample",
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List("TiTvVariantEvaluator", "CountVariants", "CompOverlap"),
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List("Sample"))
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add(new ExomeQCRScript(evalVCF))
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}
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}
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def createEval(evalVCF: File, prefix: String, evalModules: List[String], extraStrats: List[String]) {
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val eval = new Eval(evalVCF)
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eval.out = swapExt(evalVCF,".vcf", prefix + ".eval")
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eval.evalModule = evalModules
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eval.stratificationModule = List("EvalRod", "CompRod", "Novelty") ::: extraStrats
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add(eval)
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}
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class Eval(@Input vcf: File) extends VariantEval with UNIVERSAL_GATK_ARGS {
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this.rodBind :+= RodBind("eval", "VCF", vcf)
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if ( dbSNP.exists() )
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this.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
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this.doNotUseAllStandardStratifications = true
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this.doNotUseAllStandardModules = true
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this.intervalsString = List(myIntervals);
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}
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class ExomeQCRScript(vcf: File) extends CommandLineFunction {
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@Output var pdf: File = swapExt(vcf,".vcf", ".pdf")
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val root = swapExt(vcf,".vcf", "") // remove the prefix
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def commandLine = "Rscript %s/exomeQC.R %s %s %s".format(RPath, root, root, pdf)
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}
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}
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