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biopet.biopet
Commits
5d18d629
Commit
5d18d629
authored
Oct 19, 2015
by
Wai Yi Leung
Browse files
Adjusting the Sambamba view filter, exclude "split reads" in RNA-seq experiments
parent
8c039f3d
Changes
1
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public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala
View file @
5d18d629
...
...
@@ -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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