Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
bc3e6582
Commit
bc3e6582
authored
Nov 08, 2014
by
Peter van 't Hof
Browse files
Style fix
parent
384e5667
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-framework/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
View file @
bc3e6582
...
...
@@ -2,7 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.
{
BiopetQScript
,
PipelineCommand
}
import
java.io.File
import
nl.lumc.sasc.biopet.tools.
{
MpileupToVcf
,
VcfFilter
,
MergeAlleles
}
import
nl.lumc.sasc.biopet.tools.
{
MpileupToVcf
,
VcfFilter
,
MergeAlleles
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.
{
AnalyzeCovariates
,
BaseRecalibrator
,
GenotypeGVCFs
,
HaplotypeCaller
,
IndelRealigner
,
PrintReads
,
RealignerTargetCreator
,
SelectVariants
,
CombineVariants
,
UnifiedGenotyper
}
import
nl.lumc.sasc.biopet.extensions.picard.MarkDuplicates
...
...
@@ -135,7 +135,7 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
mergBuffer
+=
(
"9.raw"
->
scriptOutput
.
rawFilterVcfFile
)
if
(
useAllelesOption
.
get
)
{
val
mergeAlleles
=
MergeAlleles
(
this
,
mergeList
.
toList
,
outputDir
+
"raw.allele__temp_only.vcf.gz.tbi"
)
val
mergeAlleles
=
MergeAlleles
(
this
,
mergeList
.
toList
,
outputDir
+
"raw.allele__temp_only.vcf.gz.tbi"
)
add
(
mergeAlleles
,
isIntermediate
=
true
)
if
(
useHaplotypecaller
.
get
)
{
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment