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biopet.biopet
Commits
c8269286
Commit
c8269286
authored
Jun 10, 2014
by
Peter van 't Hof
Browse files
SplitNCigarReads now before indel realign
parent
29bf997a
Changes
1
Hide whitespace changes
Inline
Side-by-side
gatk/src/main/java/nl/lumc/sasc/biopet/pipelines/gatk/Gatk.scala
View file @
c8269286
...
...
@@ -84,9 +84,10 @@ class Gatk(private var globalConfig: Config) extends QScript with BiopetQScript
mapping
.
script
addAll
(
mapping
.
functions
)
// Add functions of mapping to curent function pool
var
bamFile
:
File
=
addIndelRealign
(
mapping
.
outputFiles
(
"finalBamFile"
),
runDir
)
// Indel realigner
bamFile
=
addBaseRecalibrator
(
bamFile
,
runDir
)
// Base recalibrator
var
bamFile
:
File
=
mapping
.
outputFiles
(
"finalBamFile"
)
if
(
inputType
==
"rna"
)
bamFile
=
addSplitNCigarReads
(
bamFile
,
runDir
)
bamFile
=
addIndelRealign
(
bamFile
,
runDir
)
// Indel realigner
bamFile
=
addBaseRecalibrator
(
bamFile
,
runDir
)
// Base recalibrator
outputFiles
+=
(
"FinalBam"
->
bamFile
)
}
else
this
.
logger
.
error
(
"Sample: "
+
sampleID
+
": No R1 found for run: "
+
runConfig
)
...
...
@@ -159,7 +160,8 @@ class Gatk(private var globalConfig: Config) extends QScript with BiopetQScript
if
(
config
.
contains
(
"scattercount"
))
this
.
scatterCount
=
config
.
getAsInt
(
"scattercount"
)
this
.
input_file
=
Seq
(
inputBam
)
this
.
out
=
swapExt
(
dir
,
inputBam
,
".bam"
,
".split.bam"
)
this
.
read_filter
:+=
"ReassignMappingQuality -DMQ 60"
this
.
read_filter
:+=
"ReassignMappingQuality"
this
.
U
=
org
.
broadinstitute
.
sting
.
gatk
.
arguments
.
ValidationExclusion
.
TYPE
.
ALLOW_N_CIGAR_READS
}
add
(
splitNCigarReads
)
...
...
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