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biopet.biopet
Commits
06a147a3
Commit
06a147a3
authored
Apr 06, 2017
by
Peter van 't Hof
Browse files
Adding bqsr implementation
parent
f4458933
Changes
2
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Inline
Side-by-side
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerAllele.scala
View file @
06a147a3
...
...
@@ -20,7 +20,7 @@
package
nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import
nl.lumc.sasc.biopet.extensions.gatk
import
nl.lumc.sasc.biopet.
utils.Logging
import
nl.lumc.sasc.biopet.
extensions.gatk.BqsrGather
import
nl.lumc.sasc.biopet.utils.config.Configurable
/** Allele mode for Haplotypecaller */
...
...
@@ -33,6 +33,13 @@ class HaplotypeCallerAllele(val parent: Configurable) extends Variantcaller {
def
biopetScript
()
{
val
hc
=
gatk
.
HaplotypeCaller
(
this
,
inputBams
.
values
.
toList
,
outputFile
)
hc
.
alleles
=
Some
(
alleles
)
hc
.
BQSR
=
if
(
inputBqsrFiles
.
isEmpty
)
None
else
{
val
gather
=
new
BqsrGather
gather
.
inputBqsrFiles
=
inputBqsrFiles
.
values
.
toList
gather
.
outputBqsrFile
=
new
File
(
outputDir
,
"bqsr.merge"
)
add
(
gather
)
Some
(
gather
.
outputBqsrFile
)
}
hc
.
genotyping_mode
=
Some
(
"GENOTYPE_GIVEN_ALLELES"
)
add
(
hc
)
}
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/UnifiedGenotyperAllele.scala
View file @
06a147a3
...
...
@@ -20,6 +20,7 @@
package
nl.lumc.sasc.biopet.pipelines.shiva.variantcallers
import
nl.lumc.sasc.biopet.extensions.gatk
import
nl.lumc.sasc.biopet.extensions.gatk.BqsrGather
import
nl.lumc.sasc.biopet.utils.config.Configurable
/** Allele mode for GenotyperAllele */
...
...
@@ -33,6 +34,13 @@ class UnifiedGenotyperAllele(val parent: Configurable) extends Variantcaller {
val
ug
=
gatk
.
UnifiedGenotyper
(
this
,
inputBams
.
values
.
toList
,
outputFile
)
ug
.
alleles
=
Some
(
alleles
)
ug
.
genotyping_mode
=
Some
(
"GENOTYPE_GIVEN_ALLELES"
)
ug
.
BQSR
=
if
(
inputBqsrFiles
.
isEmpty
)
None
else
{
val
gather
=
new
BqsrGather
gather
.
inputBqsrFiles
=
inputBqsrFiles
.
values
.
toList
gather
.
outputBqsrFile
=
new
File
(
outputDir
,
"bqsr.merge"
)
add
(
gather
)
Some
(
gather
.
outputBqsrFile
)
}
add
(
ug
)
}
}
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