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biopet.biopet
Commits
6ac5e2c8
Commit
6ac5e2c8
authored
Nov 17, 2014
by
Peter van 't Hof
Browse files
format
parent
3b0bbaf7
Changes
1
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Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @
6ac5e2c8
...
...
@@ -24,11 +24,10 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
defaults
++=
Map
(
"ploidy"
->
1
,
"use_haplotypecaller"
->
false
,
"use_unifiedgenotyper"
->
true
,
"joint_variantcalling"
->
true
)
var
gatkPipeline
:
GatkPipeline
=
_
var
gatkPipeline
:
GatkPipeline
=
new
GatkPipeline
(
this
)
gatkPipeline
.
jointVariantcalling
=
true
def
init
()
{
gatkPipeline
=
new
GatkPipeline
(
this
)
gatkPipeline
.
outputDir
=
outputDir
gatkPipeline
.
init
}
...
...
@@ -51,7 +50,7 @@ class Basty(val root: Configurable) extends QScript with MultiSampleQScript {
add
(
catConsensus
)
val
catConsensusSnps
=
Cat
(
this
,
refVariantSnps
.
consensus
::
samplesOutput
.
map
(
_
.
_2
.
outputSnps
.
consensus
).
toList
,
outputDir
+
"fastas/consensus.snps_only.fasta"
)
add
(
catConsensusSnps
)
val
catConsensusVariants
=
Cat
(
this
,
refVariants
.
consensusVariants
::
samplesOutput
.
map
(
_
.
_2
.
output
.
consensusVariants
).
toList
,
outputDir
+
"fastas/consensus.variant.fasta"
)
add
(
catConsensusVariants
)
val
catConsensusVariantsSnps
=
Cat
(
this
,
refVariantSnps
.
consensusVariants
::
samplesOutput
.
map
(
_
.
_2
.
outputSnps
.
consensusVariants
).
toList
,
outputDir
+
"fastas/consensus.variant.snps_only.fasta"
)
...
...
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