79 lines
2.1 KiB
Scala
Executable File
79 lines
2.1 KiB
Scala
Executable File
import org.broadinstitute.sting.queue.QScript._
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// Other imports can be added here
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setArgs(args)
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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 below
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val gvc = new GenerateVariantClusters
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val vr = new VariantRecalibrator
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gvc.maxGaussians = g
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gvc.shrinkage = s
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gvc.dirichlet = d
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gvc.clusterFile = new File("g%d_s%.6f_d%.6f_b%.2f.cluster".format(g,s,d,b))
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gvc.jobOutputFile = swapExt(gvc.clusterFile, ".cluster", ".gvc.out")
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vr.clusterFile = gvc.clusterFile
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vr.jobOutputFile = swapExt(vr.clusterFile, ".cluster", ".vr.out")
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vr.backOff = b
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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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// Populate parameters passed in via -P
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setParams
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// Run the pipeline
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run
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// A very basic GATK UnifiedGenotyper
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class GenerateVariantClusters extends GatkFunction {
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var maxGaussians: Int = _
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var shrinkage: Double = _
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var dirichlet: Double = _
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@Output
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var clusterFile: File = _
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def commandLine = gatkCommandLine("GenerateVariantClusters") +
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"-B input20,VCF,/broad/shptmp/rpoplin/CEUTSI.chr20.filtered.vcf " +
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"-l INFO -L 20 -an QD -an SB -an HaplotypeScore -an HRun " +
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"-resources /humgen/gsa-scr1/rpoplin/sting_dev_vb/R/ " +
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"-mG %d ".format(maxGaussians) +
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"-shrinkage %.6f ".format(shrinkage) +
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"-dirichlet %.6f ".format(dirichlet) +
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"-clusterFile %s".format(clusterFile)
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}
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// A basic GATK VariantFiltration
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class VariantRecalibrator extends GatkFunction {
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var backOff: Double = _
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@Input
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var clusterFile: File = _
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def commandLine = gatkCommandLine("VariantRecalibrator") +
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"-B input20,VCF,/broad/shptmp/rpoplin/CEUTSI.chr20.filtered.vcf " +
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"-l INFO -L 20 -titv 2.1 " +
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"--ignore_filter HARD_TO_VALIDATE " +
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"-resources /humgen/gsa-scr1/rpoplin/sting_dev_vb/R/ " +
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"-backOff %.2f ".format(backOff) +
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"-clusterFile %s ".format(clusterFile) +
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"-output %s".format(clusterFile)
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}
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