HaplotypeCallerAllele.scala 824 Bytes
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/**
 * Due to the license issue with GATK, this part of Biopet can only be used inside the
 * LUMC. Please refer to https://git.lumc.nl/biopet/biopet/wikis/home for instructions
 * on how to use this protected part of biopet or contact us at sasc@lumc.nl
 */
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package nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
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import nl.lumc.sasc.biopet.extensions.gatk.broad
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import nl.lumc.sasc.biopet.utils.config.Configurable
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/** Allele mode for Haplotypecaller */
class HaplotypeCallerAllele(val root: Configurable) extends Variantcaller {
  val name = "haplotypecaller_allele"
  protected def defaultPrio = 5

  def biopetScript() {
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    val hc = broad.HaplotypeCaller(this, inputBams.values.toList, outputFile)
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    hc.alleles = config("input_alleles")
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    hc.genotyping_mode = Some("GENOTYPE_GIVEN_ALLELES")
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    add(hc)
  }
}