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biopet.biopet
Commits
25ee758d
Commit
25ee758d
authored
Feb 26, 2015
by
Peter van 't Hof
Browse files
Adding UnifiedGenotyper
parent
3c2bd820
Changes
3
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protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaGatk.scala
View file @
25ee758d
...
...
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.broad._
import
nl.lumc.sasc.biopet.pipelines.shiva.
{
ShivaVariantcallingTrait
,
ShivaVariantcalling
,
ShivaTrait
}
import
nl.lumc.sasc.biopet.pipelines.shiva.
{
ShivaVariantcallingTrait
,
ShivaVariantcalling
,
ShivaTrait
}
import
org.broadinstitute.gatk.queue.QScript
/**
...
...
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/ShivaVariantcallingGatk.scala
View file @
25ee758d
...
...
@@ -2,7 +2,6 @@ package nl.lumc.sasc.biopet.pipelines.gatk
import
nl.lumc.sasc.biopet.core.PipelineCommand
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.broad.HaplotypeCaller
import
nl.lumc.sasc.biopet.pipelines.shiva.ShivaVariantcallingTrait
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -13,9 +12,9 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
qscript
=>
def
this
()
=
this
(
null
)
override
def
callers
=
new
Haplotype
c
aller
::
super
.
callers
override
def
callers
=
new
UnifiedGenotyper
::
new
Haplotype
C
aller
::
super
.
callers
class
Haplotype
c
aller
extends
Variantcaller
{
class
Haplotype
C
aller
extends
Variantcaller
{
val
name
=
"haplotypecaller"
protected
val
defaultPrio
=
1
protected
val
defaultUse
=
true
...
...
@@ -23,7 +22,22 @@ class ShivaVariantcallingGatk(val root: Configurable) extends QScript with Shiva
def
outputFile
=
new
File
(
outputDir
,
namePrefix
+
"haplotypecaller.vcf.gz"
)
def
addJobs
()
{
val
hc
=
new
HaplotypeCaller
(
qscript
)
val
hc
=
new
nl
.
lumc
.
sasc
.
biopet
.
extensions
.
gatk
.
broad
.
HaplotypeCaller
(
qscript
)
hc
.
input_file
=
inputBams
hc
.
out
=
outputFile
add
(
hc
)
}
}
class
UnifiedGenotyper
extends
Variantcaller
{
val
name
=
"unifiedgenotyper"
protected
val
defaultPrio
=
20
protected
val
defaultUse
=
false
def
outputFile
=
new
File
(
outputDir
,
namePrefix
+
"unifiedgenotyper.vcf.gz"
)
def
addJobs
()
{
val
hc
=
new
nl
.
lumc
.
sasc
.
biopet
.
extensions
.
gatk
.
broad
.
UnifiedGenotyper
(
qscript
)
hc
.
input_file
=
inputBams
hc
.
out
=
outputFile
add
(
hc
)
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcallingTrait.scala
View file @
25ee758d
...
...
@@ -23,8 +23,8 @@ trait ShivaVariantcallingTrait extends SummaryQScript with SampleLibraryTag {
def
namePrefix
:
String
=
{
(
sampleId
,
libId
)
match
{
case
(
Some
(
sampleId
),
Some
(
libId
))
=>
sampleId
+
"-"
+
libId
+
"."
case
(
Some
(
sampleId
),
_
)
=>
sampleId
+
"."
case
_
=>
""
case
(
Some
(
sampleId
),
_
)
=>
sampleId
+
"."
case
_
=>
""
}
}
...
...
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