diff --git a/scala/qscript/oneoffs/rpoplin/variantRecalibrator.scala b/scala/qscript/oneoffs/rpoplin/variantRecalibrator.scala deleted file mode 100755 index 4ec898ba8..000000000 --- a/scala/qscript/oneoffs/rpoplin/variantRecalibrator.scala +++ /dev/null @@ -1,55 +0,0 @@ -import org.broadinstitute.sting.queue.extensions.gatk._ -import org.broadinstitute.sting.queue.QScript - -class variantRecalibrator extends QScript { - @Argument(doc="gatkJarFile") - var gatkJarFile: File = _ - - def script = { - -val gList = List(30) -val sList = List(0.0001, 0.01) -val dList = List(0.0001, 1000.0) -val bList = List(1.0, 1.3) - -for (g: Int <- gList) { - for (s: Double <- sList) { - for (d: Double <- dList) { - for(b: Double <- bList) { - - // Using classes defined by QueueGATKExtensions.jar - val gvc = new GenerateVariantClusters - val vr = new VariantRecalibrator - - gvc.jarFile = gatkJarFile - gvc.rodBind :+= RodBind("input20", "VCF", new File("/broad/shptmp/rpoplin/CEUTSI.chr20.filtered.vcf")) - gvc.logging_level = "INFO" - gvc.intervalsString :+= "20" - gvc.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun") - gvc.maxGaussians = Some(g) - gvc.shrinkage = Some(s) - gvc.shrinkageFormat = "%.6f" - gvc.dirichlet = Some(d) - gvc.dirichletFormat = "%.6f" - gvc.clusterFile = new File("g%d_s%.6f_d%.6f_b%.2f.cluster".format(g,s,d,b)) - gvc.jobOutputFile = swapExt(gvc.clusterFile, ".cluster", ".gvc.out") - - vr.jarFile = gatkJarFile - vr.rodBind :+= RodBind("input20", "VCF", new File("/broad/shptmp/rpoplin/CEUTSI.chr20.filtered.vcf")) - vr.logging_level = "INFO" - vr.intervalsString :+= "20" - vr.target_titv = 2.1 - vr.ignore_filter :+= "HARD_TO_VALIDATE" - vr.path_to_resources = "/humgen/gsa-scr1/rpoplin/sting_dev_vb/R/" - vr.clusterFile = gvc.clusterFile - vr.jobOutputFile = swapExt(vr.clusterFile, ".cluster", ".vr.out") - vr.backOff = Some(b) - vr.backOffFormat = "%.2f" - - add(gvc, vr) - } - } - } -} - } -}