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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5450 348d0f76-0448-11de-a6fe-93d51630548a
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rpoplin 2011-03-15 22:47:55 +00:00
parent e2e435d52c
commit 9c413fbc9e
1 changed files with 0 additions and 55 deletions
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55
scala/qscript/oneoffs/rpoplin/variantRecalibrator.scala
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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)
}
}
}
}
}
}