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biopet.biopet
Commits
a34e6b23
Commit
a34e6b23
authored
Apr 06, 2017
by
Peter van 't Hof
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parent
b43464ed
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shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
...ain/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
+2
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shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/Shiva.scala
View file @
a34e6b23
...
...
@@ -248,8 +248,8 @@ class Shiva(val parent: Configurable) extends QScript with MultisampleMappingTra
if
(!
usePrintReads
)
{
import
variantcallers._
if
(
vc
.
callers
.
exists
(
_
match
{
case
_:
HaplotypeCaller
|
_
:HaplotypeCallerAllele
|
_
:
HaplotypeCallerGvcf
=>
false
case
_:
UnifiedGenotyper
|
_
:
UnifiedGenotyperAllele
=>
false
case
_:
HaplotypeCaller
|
_
:
HaplotypeCallerAllele
|
_
:
HaplotypeCallerGvcf
=>
false
case
_:
UnifiedGenotyper
|
_
:
UnifiedGenotyperAllele
=>
false
case
_
=>
true
}))
logger
.
warn
(
"Not all variantcallers chosen can read BQSR files, All non-GATK"
)
}
...
...
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