57 lines
1.6 KiB
Scala
57 lines
1.6 KiB
Scala
import org.broadinstitute.sting.queue.extensions.gatk._
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import org.broadinstitute.sting.queue.QScript
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class UnifiedGenotyperExample extends QScript {
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qscript =>
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@Input(doc="gatk jar file")
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var gatkJar: File = _
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@Input(doc="bam files", shortName="I")
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var bamFiles: List[File] = Nil
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@Input(doc="interval list", shortName="L")
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var intervals: File = _
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@Input(doc="referenceFile", shortName="R")
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var referenceFile: File = _
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@Argument(doc="filter names", shortName="filter")
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var filterNames: List[String] = Nil
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@Argument(doc="filter expressions", shortName="filterExpression")
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var filterExpressions: List[String] = Nil
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@Argument(doc="job queue", shortName="queue", required=false)
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var jobQueue = "broad"
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trait UnifiedGenotyperArguments extends CommandLineGATK {
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this.jobQueue = qscript.jobQueue
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this.jarFile = qscript.gatkJar
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this.intervals = qscript.intervals
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this.reference_sequence = qscript.referenceFile
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}
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def script = {
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for (bam <- bamFiles) {
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val ug = new UnifiedGenotyper with UnifiedGenotyperArguments
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val vf = new VariantFiltration with UnifiedGenotyperArguments
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val ve = new VariantEval with UnifiedGenotyperArguments
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// Make sure the Sting/shell folder is in your path to use mergeText.sh and splitIntervals.sh.
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ug.scatterCount = 3
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ug.cleanupTempDirectories = true
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ug.input_file :+= bam
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ug.out = swapExt(bam, "bam", "unfiltered.vcf")
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vf.rodBind :+= RodBind("vcf", "VCF", ug.out)
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vf.out = swapExt(bam, "bam", "filtered.vcf")
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ve.rodBind :+= RodBind("vcf", "VCF", vf.out)
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ve.out = swapExt(bam, "bam", "eval")
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add(ug, vf, ve)
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}
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}
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}
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