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biopet.biopet
Commits
5121ff20
Commit
5121ff20
authored
Feb 04, 2015
by
Peter van 't Hof
Browse files
Added vcfstats to gatk pipeline
parent
25a8db4f
Changes
2
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protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/GatkVariantcalling.scala
View file @
5121ff20
...
...
@@ -7,7 +7,7 @@ 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.
{
VcfStats
,
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
...
...
@@ -197,6 +197,12 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
val
cvFinal
=
CombineVariants
(
this
,
mergeList
.
toList
,
outputDir
+
outputName
+
".final.vcf.gz"
)
cvFinal
.
genotypemergeoption
=
org
.
broadinstitute
.
gatk
.
utils
.
variant
.
GATKVariantContextUtils
.
GenotypeMergeType
.
UNSORTED
add
(
cvFinal
)
val
vcfStats
=
new
VcfStats
(
this
)
vcfStats
.
input
=
cvFinal
.
out
vcfStats
.
setOutputDir
(
outputDir
+
File
.
separator
+
"vcfstats"
)
add
(
vcfStats
)
scriptOutput
.
finalVcfFile
=
cvFinal
.
out
}
}
...
...
public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala
View file @
5121ff20
...
...
@@ -22,7 +22,14 @@ class VcfStats(val root: Configurable) extends BiopetJavaCommandLineFunction {
var
input
:
File
=
_
@Output
(
doc
=
"Output fastq"
,
shortName
=
"o"
,
required
=
true
)
var
output
:
File
=
_
protected
var
generalTsv
:
File
=
_
protected
var
outputDir
:
String
=
_
def
setOutputDir
(
dir
:
String
)
:
Unit
=
{
outputDir
=
dir
generalTsv
=
new
File
(
dir
+
File
.
separator
+
"genotype_general.tsv"
)
}
/**
* Creates command to execute extension
...
...
@@ -30,7 +37,7 @@ class VcfStats(val root: Configurable) extends BiopetJavaCommandLineFunction {
*/
override
def
commandLine
=
super
.
commandLine
+
required
(
"-I"
,
input
)
+
required
(
"-o"
,
output
)
required
(
"-o"
,
output
Dir
)
}
object
VcfStats
extends
ToolCommand
{
...
...
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