No default limitation on variantcalling when target_bed is given

protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkPipeline.scala

@@ -49,9 +49,6 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
   }
 
   def init() {
-    if (config.contains("target_bed")) {
-      defaults ++= Map("gatk" -> Map(("intervals" -> config("target_bed").asStringList)))
-    }
     if (config.contains("gvcfFiles"))
       for (file <- config("gvcfFiles").asList)
         gvcfFiles :+= file.toString

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/MpileupToVcf.scala

@@ -35,8 +35,7 @@ class MpileupToVcf(val root: Configurable) extends BiopetJavaCommandLineFunction
   override val defaultVmem = "6G"
   memoryLimit = Option(2.0)
 
-  if (config.contains("target_bed")) defaults ++= Map("samtoolsmpileup" -> Map("interval_bed" -> config("target_bed").asStringList.head,
-    "disable_baq" -> true, "min_map_quality" -> 1))
+  defaults ++= Map("samtoolsmpileup" -> Map("disable_baq" -> true, "min_map_quality" -> 1))
 
   override def afterGraph {
     super.afterGraph