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biopet.biopet
Commits
f6bbd1b0
Commit
f6bbd1b0
authored
Aug 22, 2014
by
Peter van 't Hof
Browse files
Added allSitePLs option
parent
f66115cc
Changes
1
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gatk/gatk-variantcalling/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
View file @
f6bbd1b0
...
...
@@ -131,7 +131,9 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
logger
.
warn
(
"BamOutput is on, nct/threads is forced to set on 1, this option is only for debug"
)
}
this
.
memoryLimit
=
this
.
nct
*
2
if
(
configContains
(
"allSitePLs"
))
this
.
allSitePLs
=
config
(
"allSitePLs"
)
// GVCF options
if
(
gvcfMode
)
{
this
.
emitRefConfidence
=
org
.
broadinstitute
.
gatk
.
tools
.
walkers
.
haplotypecaller
.
ReferenceConfidenceMode
.
GVCF
...
...
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