HaplotypeCallerAllele.scala 719 Bytes
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package nl.lumc.sasc.biopet.pipelines.gatk.variantcallers

import nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
import nl.lumc.sasc.biopet.utils.config.Configurable

/** Allele mode for Haplotypecaller */
class HaplotypeCallerAllele(val root: Configurable) extends Variantcaller {
  val name = "haplotypecaller_allele"
  protected def defaultPrio = 5

  def biopetScript() {
    val hc = new nl.lumc.sasc.biopet.extensions.gatk.broad.HaplotypeCaller(this)
    hc.input_file = inputBams.values.toList
    hc.out = outputFile
    hc.alleles = config("input_alleles")
    hc.genotyping_mode = org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES
    add(hc)
  }
}