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biopet.biopet
Commits
f17e2175
Commit
f17e2175
authored
Oct 19, 2015
by
Sander van der Zeeuw
Browse files
added dependency for combinevariants
parent
34024cc5
Changes
2
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public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
View file @
f17e2175
...
...
@@ -53,6 +53,8 @@ class CombineVariants(val root: Configurable) extends Gatk {
case
Some
(
"UNIQUIFY"
)
|
Some
(
"PRIORITIZE"
)
|
Some
(
"UNSORTED"
)
|
Some
(
"REQUIRE_UNIQUE"
)
|
None
=>
case
_
=>
throw
new
IllegalArgumentException
(
"Wrong option for genotypeMergeOptions"
)
}
deps
:::=
inputFiles
.
filter
(
_
.
getName
.
endsWith
(
"vcf.gz"
)).
map
(
x
=>
new
File
(
x
.
getAbsolutePath
+
".tbi"
))
deps
=
deps
.
distinct
}
override
def
cmdLine
=
super
.
cmdLine
+
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
View file @
f17e2175
...
...
@@ -18,15 +18,14 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import
java.io.File
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.
{
Reference
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.bcftools.
{
Bcftools
Merge
,
Bcftools
Call
}
import
nl.lumc.sasc.biopet.core.
{
Reference
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.extensions.bcftools.
{
Bcftools
Call
,
Bcftools
Merge
}
import
nl.lumc.sasc.biopet.extensions.gatk.CombineVariants
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsMpileup
import
nl.lumc.sasc.biopet.extensions.tools.
{
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.extensions.
{
Bgzip
,
Tabix
}
import
nl.lumc.sasc.biopet.utils.
{
ConfigUtils
,
Logging
}
import
org.broadinstitute.gatk.queue.function.CommandLineFunction
import
org.broadinstitute.gatk.utils.commandline.
{
Input
,
Output
}
import
nl.lumc.sasc.biopet.extensions.tools.
{
MpileupToVcf
,
VcfFilter
,
VcfStats
}
import
nl.lumc.sasc.biopet.extensions.
{
Bgzip
,
Tabix
}
import
nl.lumc.sasc.biopet.utils.Logging
import
org.broadinstitute.gatk.utils.commandline.Input
/**
* Common trait for ShivaVariantcalling
...
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