Commit 09bf4a36 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

No default limitation on variantcalling when target_bed is given

parent ecff240c
...@@ -49,9 +49,6 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri ...@@ -49,9 +49,6 @@ class GatkPipeline(val root: Configurable) extends QScript with MultiSampleQScri
} }
def init() { def init() {
if (config.contains("target_bed")) {
defaults ++= Map("gatk" -> Map(("intervals" -> config("target_bed").asStringList)))
}
if (config.contains("gvcfFiles")) if (config.contains("gvcfFiles"))
for (file <- config("gvcfFiles").asList) for (file <- config("gvcfFiles").asList)
gvcfFiles :+= file.toString gvcfFiles :+= file.toString
......
...@@ -35,8 +35,7 @@ class MpileupToVcf(val root: Configurable) extends BiopetJavaCommandLineFunction ...@@ -35,8 +35,7 @@ class MpileupToVcf(val root: Configurable) extends BiopetJavaCommandLineFunction
override val defaultVmem = "6G" override val defaultVmem = "6G"
memoryLimit = Option(2.0) memoryLimit = Option(2.0)
if (config.contains("target_bed")) defaults ++= Map("samtoolsmpileup" -> Map("interval_bed" -> config("target_bed").asStringList.head, defaults ++= Map("samtoolsmpileup" -> Map("disable_baq" -> true, "min_map_quality" -> 1))
"disable_baq" -> true, "min_map_quality" -> 1))
override def afterGraph { override def afterGraph {
super.afterGraph super.afterGraph
......
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