57 lines
1.9 KiB
Scala
Executable File
57 lines
1.9 KiB
Scala
Executable File
import org.broadinstitute.sting.queue.extensions.gatk._
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import org.broadinstitute.sting.queue.QScript
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class variantRecalibrator extends QScript {
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@Argument(doc="gatkJarFile")
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var gatkJarFile: File = _
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def script = {
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val gList = List(30)
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val sList = List(0.0001, 0.01)
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val dList = List(0.0001, 1000.0)
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val bList = List(1.0, 1.3)
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for (g: Int <- gList) {
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for (s: Double <- sList) {
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for (d: Double <- dList) {
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for(b: Double <- bList) {
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// Using classes defined by QueueGATKExtensions.jar
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val gvc = new GenerateVariantClusters
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val vr = new VariantRecalibrator
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gvc.jarFile = gatkJarFile
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gvc.rodBind :+= RodBind("input20", "VCF", new File("/broad/shptmp/rpoplin/CEUTSI.chr20.filtered.vcf"))
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gvc.logging_level = "INFO"
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gvc.intervalsString :+= "20"
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gvc.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
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gvc.path_to_resources = "/humgen/gsa-scr1/rpoplin/sting_dev_vb/R/"
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gvc.maxGaussians = Some(g)
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gvc.shrinkage = Some(s)
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gvc.shrinkageFormat = "%.6f"
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gvc.dirichlet = Some(d)
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gvc.dirichletFormat = "%.6f"
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gvc.clusterFile = "g%d_s%.6f_d%.6f_b%.2f.cluster".format(g,s,d,b)
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gvc.jobOutputFile = new File(gvc.clusterFile.stripSuffix(".cluster") + ".gvc.out")
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vr.jarFile = gatkJarFile
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vr.rodBind :+= RodBind("input20", "VCF", new File("/broad/shptmp/rpoplin/CEUTSI.chr20.filtered.vcf"))
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vr.logging_level = "INFO"
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vr.intervalsString :+= "20"
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vr.target_titv = Some(2.1)
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vr.ignore_filter :+= "HARD_TO_VALIDATE"
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vr.path_to_resources = "/humgen/gsa-scr1/rpoplin/sting_dev_vb/R/"
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vr.clusterFile = gvc.clusterFile
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vr.jobOutputFile = new File(vr.clusterFile.stripSuffix(".cluster") + ".vr.out")
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vr.backOff = Some(b)
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vr.backOffFormat = "%.2f"
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add(gvc, vr)
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}
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}
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}
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}
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}
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}
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