HaplotypeCallerAllele.scala 889 Bytes
Newer Older
Peter van 't Hof's avatar
Peter van 't Hof committed
1
2
3
4
5
/**
 * 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
 */
6
7
8
9
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
10
import nl.lumc.sasc.biopet.extensions.gatk.broad
11
12
13
14
15
16
17

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

  def biopetScript() {
18
    val hc = broad.HaplotypeCaller(this, inputBams.values.toList, outputFile)
19
    hc.alleles = config("input_alleles")
Peter van 't Hof's avatar
Peter van 't Hof committed
20
    hc.genotyping_mode = "GENOTYPE_GIVEN_ALLELES"
21
22
23
    add(hc)
  }
}