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biopet.biopet
Commits
e57304d0
Commit
e57304d0
authored
Apr 27, 2016
by
Peter van 't Hof
Browse files
Fixed type
parent
a508e6f8
Changes
1
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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/HaplotypeCaller.scala
View file @
e57304d0
...
...
@@ -512,7 +512,7 @@ object HaplotypeCaller {
def
gvcf
(
root
:
Configurable
,
inputFile
:
File
,
outputFile
:
File
)
:
HaplotypeCaller
=
{
val
hc
=
apply
(
root
,
List
(
inputFile
),
outputFile
)
hc
.
emitRefConfidence
=
"GVCF"
hc
.
variant_index_type
=
GATKVCFIndexType
.
LINEAR
hc
.
variant_index_type
=
Some
(
"
LINEAR
"
)
hc
.
variant_index_parameter
=
Some
(
hc
.
config
(
"variant_index_parameter"
,
default
=
128000
).
asInt
)
hc
}
...
...
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