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biopet.biopet
Commits
f841b758
Commit
f841b758
authored
Jun 03, 2016
by
Peter van 't Hof
Browse files
Fix shiva variantcalling
parent
9461ff47
Changes
2
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shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerAllele.scala
View file @
f841b758
...
...
@@ -28,7 +28,7 @@ class HaplotypeCallerAllele(val root: Configurable) extends Variantcaller {
val
name
=
"haplotypecaller_allele"
protected
def
defaultPrio
=
5
val
alleles
:
File
=
config
(
"input_alleles"
)
lazy
val
alleles
:
File
=
config
(
"input_alleles"
)
def
biopetScript
()
{
val
hc
=
gatk
.
HaplotypeCaller
(
this
,
inputBams
.
values
.
toList
,
outputFile
)
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/UnifiedGenotyperAllele.scala
View file @
f841b758
...
...
@@ -27,7 +27,7 @@ class UnifiedGenotyperAllele(val root: Configurable) extends Variantcaller {
val
name
=
"unifiedgenotyper_allele"
protected
def
defaultPrio
=
9
val
alleles
:
File
=
config
(
"input_alleles"
)
lazy
val
alleles
:
File
=
config
(
"input_alleles"
)
def
biopetScript
()
{
val
ug
=
gatk
.
UnifiedGenotyper
(
this
,
inputBams
.
values
.
toList
,
outputFile
)
...
...
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