Commit 5d18d629 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Adjusting the Sambamba view filter, exclude "split reads" in RNA-seq experiments

parent 8c039f3d
......@@ -69,7 +69,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript {
// sambamba view -f bam -F "unmapped or mate_is_unmapped" <alnFile> > <extracted.bam>
val samFilterUnmapped = new SambambaView(qscript)
samFilterUnmapped.input = bamfile
samFilterUnmapped.filter = Some("(unmapped or mate_is_unmapped) and not (secondary_alignment)")
samFilterUnmapped.filter = Some("(unmapped or mate_is_unmapped) and not (secondary_alignment) and [XH] == null")
samFilterUnmapped.output = new File(outputDir, s"$outputName.unmapped.bam")
samFilterUnmapped.isIntermediate = false
add(samFilterUnmapped)
......
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