UnifiedGenotyper.scala 532 Bytes
Newer Older
1
2
3
4
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
Peter van 't Hof's avatar
Peter van 't Hof committed
5
import nl.lumc.sasc.biopet.extensions.gatk.broad
6
7
8
9
10
11
12

/** Default mode for UnifiedGenotyper */
class UnifiedGenotyper(val root: Configurable) extends Variantcaller {
  val name = "unifiedgenotyper"
  protected def defaultPrio = 20

  def biopetScript() {
Peter van 't Hof's avatar
Peter van 't Hof committed
13
    val ug = broad.UnifiedGenotyper(this, inputBams.values.toList, outputFile)
14
15
16
    add(ug)
  }
}