Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
5dad53d7
Commit
5dad53d7
authored
Jan 23, 2015
by
Wai Yi Leung
Browse files
Generate bamstats on the dedup
parent
e1eb4765
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/yamsvp/src/main/scala/nl/lumc/sasc/biopet/pipelines/yamsvp/Yamsvp.scala
View file @
5dad53d7
...
...
@@ -28,6 +28,7 @@ import nl.lumc.sasc.biopet.extensions.igvtools.IGVToolsCount
import
nl.lumc.sasc.biopet.extensions.sambamba.
{
SambambaIndex
,
SambambaMerge
,
SambambaMarkdup
}
import
nl.lumc.sasc.biopet.extensions.svcallers.pindel.Pindel
import
nl.lumc.sasc.biopet.extensions.svcallers.
{
Breakdancer
,
Delly
,
CleverCaller
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BamMetrics
import
nl.lumc.sasc.biopet.pipelines.mapping.Mapping
...
...
@@ -94,19 +95,21 @@ class Yamsvp(val root: Configurable) extends QScript with MultiSampleQScript {
// When the sample has only 1 run, make a link in the main alignment directory
val
alignmentlink
=
Ln
(
this
,
libraryBamfiles
.
head
,
alignmentDir
+
sampleID
+
".merged.bam"
,
true
)
add
(
alignmentlink
,
isIntermediate
=
true
)
add
(
alignmentlink
,
isIntermediate
=
true
)
alignmentlink
.
out
}
else
if
(
libraryBamfiles
.
size
>
1
)
{
val
mergeSamFiles
=
new
SambambaMerge
(
this
)
mergeSamFiles
.
input
=
libraryBamfiles
mergeSamFiles
.
output
=
alignmentDir
+
sampleID
+
".merged.bam"
add
(
mergeSamFiles
,
isIntermediate
=
true
)
add
(
mergeSamFiles
,
isIntermediate
=
true
)
mergeSamFiles
.
output
}
else
null
val
bamMarkDup
=
SambambaMarkdup
(
this
,
bamFile
)
add
(
bamMarkDup
)
addAll
(
BamMetrics
(
this
,
bamMarkDup
.
output
,
alignmentDir
+
"metrics/"
).
functions
)
// create an IGV TDF file
val
tdfCount
=
IGVToolsCount
(
this
,
bamMarkDup
.
output
,
config
(
"genomename"
,
default
=
"hg19"
))
add
(
tdfCount
)
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment