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biopet.biopet
Commits
6441dfd0
Commit
6441dfd0
authored
Nov 22, 2014
by
Peter van 't Hof
Browse files
Added protected artifact for gatk extensions
parent
34023585
Changes
19
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protected/biopet-gatk-extensions/.gitignore
0 → 100644
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6441dfd0
/target/
\ No newline at end of file
protected/biopet-gatk-extensions/pom.xml
0 → 100644
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6441dfd0
<project
xmlns=
"http://maven.apache.org/POM/4.0.0"
xmlns:xsi=
"http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation=
"http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd"
>
<modelVersion>
4.0.0
</modelVersion>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetGatkExtensions
</artifactId>
<version>
0.2.0-DEV
</version>
<packaging>
jar
</packaging>
<inceptionYear>
2014
</inceptionYear>
<name>
BiopetGatkExtensions
</name>
<url>
http://maven.apache.org
</url>
<properties>
<project.build.sourceEncoding>
UTF-8
</project.build.sourceEncoding>
<sting.unpack.phase>
prepare-package
</sting.unpack.phase>
<sting.shade.phase>
package
</sting.shade.phase>
<app.main.class>
nl.lumc.sasc.biopet.core.BiopetExecutable
</app.main.class>
</properties>
<dependencies>
<dependency>
<groupId>
nl.lumc.sasc
</groupId>
<artifactId>
BiopetFramework
</artifactId>
<version>
0.2.0-DEV
</version>
</dependency>
<dependency>
<groupId>
org.broadinstitute.gatk
</groupId>
<artifactId>
gatk-queue-extensions-distribution
</artifactId>
<version>
3.3
</version>
</dependency>
</dependencies>
<build>
<resources>
<resource>
<directory>
src/main/resources
</directory>
<includes>
<include>
**/*
</include>
</includes>
</resource>
</resources>
<plugins>
<plugin>
<groupId>
org.scala-tools
</groupId>
<artifactId>
maven-scala-plugin
</artifactId>
<version>
2.15.2
</version>
<executions>
<execution>
<id>
scala-compile
</id>
<goals>
<goal>
compile
</goal>
<goal>
testCompile
</goal>
</goals>
<configuration>
<args>
<arg>
-dependencyfile
</arg>
<arg>
${project.build.directory}/.scala_dependencies
</arg>
<arg>
-deprecation
</arg>
<arg>
-feature
</arg>
</args>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>
org.apache.maven.plugins
</groupId>
<artifactId>
maven-jar-plugin
</artifactId>
<version>
2.5
</version>
<configuration>
<archive>
<manifest>
<addDefaultImplementationEntries>
true
</addDefaultImplementationEntries>
<addDefaultSpecificationEntries>
true
</addDefaultSpecificationEntries>
</manifest>
</archive>
</configuration>
</plugin>
<plugin>
<groupId>
org.apache.maven.plugins
</groupId>
<artifactId>
maven-compiler-plugin
</artifactId>
<version>
2.3.2
</version>
<configuration>
<showDeprecation>
true
</showDeprecation>
</configuration>
</plugin>
</plugins>
</build>
</project>
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/AnalyzeCovariates.scala
0 → 100644
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6441dfd0
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
AnalyzeCovariates
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
AnalyzeCovariates
with
GatkGeneral
{
}
object
AnalyzeCovariates
{
def
apply
(
root
:
Configurable
,
before
:
File
,
after
:
File
,
plots
:
File
)
:
AnalyzeCovariates
=
{
val
ac
=
new
AnalyzeCovariates
(
root
)
ac
.
before
=
before
ac
.
after
=
after
ac
.
plots
=
plots
return
ac
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/ApplyRecalibration.scala
0 → 100644
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6441dfd0
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
ApplyRecalibration
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
ApplyRecalibration
with
GatkGeneral
{
override
def
afterGraph
{
super
.
afterGraph
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
nt
=
Option
(
getThreads
(
3
))
memoryLimit
=
Option
(
nt
.
getOrElse
(
1
)
*
2
)
ts_filter_level
=
config
(
"ts_filter_level"
)
}
}
object
ApplyRecalibration
{
def
apply
(
root
:
Configurable
,
input
:
File
,
output
:
File
,
recal_file
:
File
,
tranches_file
:
File
,
indel
:
Boolean
=
false
)
:
ApplyRecalibration
=
{
val
ar
=
if
(
indel
)
new
ApplyRecalibration
(
root
)
{
mode
=
org
.
broadinstitute
.
gatk
.
tools
.
walkers
.
variantrecalibration
.
VariantRecalibratorArgumentCollection
.
Mode
.
INDEL
defaults
++=
Map
(
"ts_filter_level"
->
99.0
)
}
else
new
ApplyRecalibration
(
root
)
{
mode
=
org
.
broadinstitute
.
gatk
.
tools
.
walkers
.
variantrecalibration
.
VariantRecalibratorArgumentCollection
.
Mode
.
SNP
defaults
++=
Map
(
"ts_filter_level"
->
99.5
)
}
ar
.
input
:+=
input
ar
.
recal_file
=
recal_file
ar
.
tranches_file
=
tranches_file
ar
.
out
=
output
return
ar
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/BaseRecalibrator.scala
0 → 100644
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6441dfd0
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
BaseRecalibrator
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
BaseRecalibrator
with
GatkGeneral
{
memoryLimit
=
Option
(
4
)
override
val
defaultVmem
=
"8G"
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
if
(
config
.
contains
(
"dbsnp"
))
knownSites
:+=
new
File
(
config
(
"dbsnp"
).
asString
)
if
(
config
.
contains
(
"known_sites"
))
knownSites
:+=
new
File
(
config
(
"known_sites"
).
asString
)
}
object
BaseRecalibrator
{
def
apply
(
root
:
Configurable
,
input
:
File
,
output
:
File
)
:
BaseRecalibrator
=
{
val
br
=
new
BaseRecalibrator
(
root
)
br
.
input_file
:+=
input
br
.
out
=
output
br
.
afterGraph
return
br
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala
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6441dfd0
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
CombineGVCFs
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
CombineGVCFs
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
}
object
CombineGVCFs
{
def
apply
(
root
:
Configurable
,
input
:
List
[
File
],
output
:
File
)
:
CombineGVCFs
=
{
val
cg
=
new
CombineGVCFs
(
root
)
cg
.
variant
=
input
cg
.
o
=
output
return
cg
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineVariants.scala
0 → 100644
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6441dfd0
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
CombineVariants
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
CombineVariants
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
}
object
CombineVariants
{
def
apply
(
root
:
Configurable
,
input
:
List
[
File
],
output
:
File
)
:
CombineVariants
=
{
val
cv
=
new
CombineVariants
(
root
)
cv
.
variant
=
input
cv
.
out
=
output
return
cv
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GatkGeneral.scala
0 → 100644
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6441dfd0
package
nl.lumc.sasc.biopet.extensions.gatk
import
nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
import
org.broadinstitute.gatk.queue.extensions.gatk.CommandLineGATK
trait
GatkGeneral
extends
CommandLineGATK
with
BiopetJavaCommandLineFunction
{
memoryLimit
=
Option
(
3
)
if
(
config
.
contains
(
"gatk_jar"
))
jarFile
=
config
(
"gatk_jar"
)
override
val
defaultVmem
=
"7G"
if
(
config
.
contains
(
"intervals"
,
submodule
=
"gatk"
))
intervals
=
config
(
"intervals"
,
submodule
=
"gatk"
).
asFileList
if
(
config
.
contains
(
"exclude_intervals"
,
submodule
=
"gatk"
))
excludeIntervals
=
config
(
"exclude_intervals"
,
submodule
=
"gatk"
).
asFileList
reference_sequence
=
config
(
"reference"
,
submodule
=
"gatk"
)
gatk_key
=
config
(
"gatk_key"
,
submodule
=
"gatk"
)
if
(
config
.
contains
(
"pedigree"
,
submodule
=
"gatk"
))
pedigree
=
config
(
"pedigree"
,
submodule
=
"gatk"
).
asFileList
}
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
0 → 100644
View file @
6441dfd0
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
GenotypeGVCFs
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
GenotypeGVCFs
with
GatkGeneral
{
annotation
++=
config
(
"annotation"
,
default
=
Seq
(
"FisherStrand"
,
"QualByDepth"
,
"ChromosomeCounts"
)).
asStringList
if
(
config
.
contains
(
"dbsnp"
))
dbsnp
=
config
(
"dbsnp"
)
if
(
config
.
contains
(
"scattercount"
,
"genotypegvcfs"
))
scatterCount
=
config
(
"scattercount"
)
if
(
config
(
"inputtype"
,
default
=
"dna"
).
asString
==
"rna"
)
{
stand_call_conf
=
config
(
"stand_call_conf"
,
default
=
20
)
stand_emit_conf
=
config
(
"stand_emit_conf"
,
default
=
0
)
}
else
{
stand_call_conf
=
config
(
"stand_call_conf"
,
default
=
30
)
stand_emit_conf
=
config
(
"stand_emit_conf"
,
default
=
0
)
}
}
object
GenotypeGVCFs
{
def
apply
(
root
:
Configurable
,
gvcfFiles
:
List
[
File
],
output
:
File
)
:
GenotypeGVCFs
=
{
val
gg
=
new
GenotypeGVCFs
(
root
)
gg
.
variant
=
gvcfFiles
gg
.
out
=
output
return
gg
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
0 → 100644
View file @
6441dfd0
package
nl.lumc.sasc.biopet.extensions.gatk
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.utils.variant.GATKVCFIndexType
class
HaplotypeCaller
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
HaplotypeCaller
with
GatkGeneral
{
override
def
afterGraph
{
super
.
afterGraph
min_mapping_quality_score
=
config
(
"minMappingQualityScore"
,
default
=
20
)
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
if
(
config
.
contains
(
"dbsnp"
))
this
.
dbsnp
=
config
(
"dbsnp"
)
this
.
sample_ploidy
=
config
(
"ploidy"
)
nct
=
config
(
"threads"
,
default
=
1
)
bamOutput
=
config
(
"bamOutput"
)
memoryLimit
=
Option
(
nct
.
getOrElse
(
1
)
*
2
)
if
(
config
.
contains
(
"allSitePLs"
))
this
.
allSitePLs
=
config
(
"allSitePLs"
)
if
(
config
.
contains
(
"output_mode"
))
{
import
org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode._
config
(
"output_mode"
).
asString
match
{
case
"EMIT_ALL_CONFIDENT_SITES"
=>
output_mode
=
EMIT_ALL_CONFIDENT_SITES
case
"EMIT_ALL_SITES"
=>
output_mode
=
EMIT_ALL_SITES
case
"EMIT_VARIANTS_ONLY"
=>
output_mode
=
EMIT_VARIANTS_ONLY
case
e
=>
logger
.
warn
(
"output mode '"
+
e
+
"' does not exist"
)
}
}
if
(
config
(
"inputtype"
,
default
=
"dna"
).
asString
==
"rna"
)
{
dontUseSoftClippedBases
=
config
(
"dontusesoftclippedbases"
,
default
=
true
)
stand_call_conf
=
config
(
"stand_call_conf"
,
default
=
5
)
stand_emit_conf
=
config
(
"stand_emit_conf"
,
default
=
0
)
}
else
{
dontUseSoftClippedBases
=
config
(
"dontusesoftclippedbases"
,
default
=
false
)
stand_call_conf
=
config
(
"stand_call_conf"
,
default
=
5
)
stand_emit_conf
=
config
(
"stand_emit_conf"
,
default
=
0
)
}
if
(
bamOutput
!=
null
&&
nct
.
getOrElse
(
1
)
>
1
)
{
nct
=
Option
(
1
)
logger
.
warn
(
"BamOutput is on, nct/threads is forced to set on 1, this option is only for debug"
)
}
}
def
useGvcf
()
{
emitRefConfidence
=
org
.
broadinstitute
.
gatk
.
tools
.
walkers
.
haplotypecaller
.
ReferenceConfidenceMode
.
GVCF
variant_index_type
=
GATKVCFIndexType
.
LINEAR
variant_index_parameter
=
config
(
"variant_index_parameter"
,
default
=
128000
)
}
}
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/IndelRealigner.scala
0 → 100644
View file @
6441dfd0
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
IndelRealigner
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
IndelRealigner
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
}
object
IndelRealigner
{
def
apply
(
root
:
Configurable
,
input
:
File
,
targetIntervals
:
File
,
outputDir
:
String
)
:
IndelRealigner
=
{
val
ir
=
new
IndelRealigner
(
root
)
ir
.
input_file
:+=
input
ir
.
targetIntervals
=
targetIntervals
ir
.
out
=
new
File
(
outputDir
,
input
.
getName
.
stripSuffix
(
".bam"
)
+
".realign.bam"
)
return
ir
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/PrintReads.scala
0 → 100644
View file @
6441dfd0
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
PrintReads
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
PrintReads
with
GatkGeneral
{
memoryLimit
=
Option
(
4
)
override
val
defaultVmem
=
"8G"
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
}
object
PrintReads
{
def
apply
(
root
:
Configurable
,
input
:
File
,
output
:
File
)
:
PrintReads
=
{
val
br
=
new
PrintReads
(
root
)
br
.
input_file
:+=
input
br
.
out
=
output
return
br
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/RealignerTargetCreator.scala
0 → 100644
View file @
6441dfd0
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
RealignerTargetCreator
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
RealignerTargetCreator
with
GatkGeneral
{
override
val
defaultVmem
=
"6G"
memoryLimit
=
Some
(
2.5
)
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
if
(
config
.
contains
(
"known"
))
known
++=
config
(
"known"
).
asFileList
}
object
RealignerTargetCreator
{
def
apply
(
root
:
Configurable
,
input
:
File
,
outputDir
:
String
)
:
RealignerTargetCreator
=
{
val
re
=
new
RealignerTargetCreator
(
root
)
re
.
input_file
:+=
input
re
.
out
=
new
File
(
outputDir
,
input
.
getName
.
stripSuffix
(
".bam"
)
+
".realign.intervals"
)
return
re
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
0 → 100644
View file @
6441dfd0
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
SelectVariants
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
SelectVariants
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
}
object
SelectVariants
{
def
apply
(
root
:
Configurable
,
input
:
File
,
output
:
File
)
:
SelectVariants
=
{
val
sv
=
new
SelectVariants
(
root
)
sv
.
variant
=
input
sv
.
out
=
output
return
sv
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
0 → 100644
View file @
6441dfd0
package
nl.lumc.sasc.biopet.extensions.gatk
import
nl.lumc.sasc.biopet.core.config.Configurable
class
UnifiedGenotyper
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
UnifiedGenotyper
with
GatkGeneral
{
override
def
afterGraph
{
super
.
afterGraph
genotype_likelihoods_model
=
org
.
broadinstitute
.
gatk
.
tools
.
walkers
.
genotyper
.
GenotypeLikelihoodsCalculationModel
.
Model
.
BOTH
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
if
(
config
.
contains
(
"dbsnp"
))
this
.
dbsnp
=
config
(
"dbsnp"
)
this
.
sample_ploidy
=
config
(
"ploidy"
)
nct
=
config
(
"threads"
,
default
=
1
)
memoryLimit
=
Option
(
nct
.
getOrElse
(
1
)
*
2
)
if
(
config
.
contains
(
"allSitePLs"
))
this
.
allSitePLs
=
config
(
"allSitePLs"
)
if
(
config
.
contains
(
"output_mode"
))
{
import
org.broadinstitute.gatk.tools.walkers.genotyper.OutputMode._
config
(
"output_mode"
).
asString
match
{
case
"EMIT_ALL_CONFIDENT_SITES"
=>
output_mode
=
EMIT_ALL_CONFIDENT_SITES
case
"EMIT_ALL_SITES"
=>
output_mode
=
EMIT_ALL_SITES
case
"EMIT_VARIANTS_ONLY"
=>
output_mode
=
EMIT_VARIANTS_ONLY
case
e
=>
logger
.
warn
(
"output mode '"
+
e
+
"' does not exist"
)
}
}
if
(
config
(
"inputtype"
,
default
=
"dna"
).
asString
==
"rna"
)
{
stand_call_conf
=
config
(
"stand_call_conf"
,
default
=
5
)
stand_emit_conf
=
config
(
"stand_emit_conf"
,
default
=
0
)
}
else
{
stand_call_conf
=
config
(
"stand_call_conf"
,
default
=
5
)
stand_emit_conf
=
config
(
"stand_emit_conf"
,
default
=
0
)
}
}
}
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala
0 → 100644
View file @
6441dfd0
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
VariantAnnotator
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
VariantAnnotator
with
GatkGeneral
{
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
dbsnp
=
config
(
"dbsnp"
)
}
object
VariantAnnotator
{
def
apply
(
root
:
Configurable
,
input
:
File
,
bamFiles
:
List
[
File
],
output
:
File
)
:
VariantAnnotator
=
{
val
va
=
new
VariantAnnotator
(
root
)
va
.
variant
=
input
va
.
input_file
=
bamFiles
va
.
out
=
output
return
va
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
0 → 100644
View file @
6441dfd0
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
class
VariantEval
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
VariantEval
with
GatkGeneral
{
override
def
afterGraph
{
super
.
afterGraph
}
}
object
VariantEval
{
def
apply
(
root
:
Configurable
,
sample
:
File
,
compareWith
:
File
,
output
:
File
)
:
VariantEval
=
{
val
vareval
=
new
VariantEval
(
root
)
vareval
.
eval
=
Seq
(
sample
)
vareval
.
comp
=
Seq
(
compareWith
)
vareval
.
out
=
output
vareval
.
afterGraph
return
vareval
}
def
apply
(
root
:
Configurable
,
sample
:
File
,
compareWith
:
File
,
output
:
File
,
ST
:
Seq
[
String
],
EV
:
Seq
[
String
])
:
VariantEval
=
{
val
vareval
=
new
VariantEval
(
root
)
vareval
.
eval
=
Seq
(
sample
)
vareval
.
comp
=
Seq
(
compareWith
)
vareval
.
out
=
output
vareval
.
noST
=
true
vareval
.
ST
=
ST
vareval
.
noEV
=
true
vareval
.
EV
=
EV
vareval
.
afterGraph
return
vareval
}
}
\ No newline at end of file
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantRecalibrator.scala
0 → 100644
View file @
6441dfd0
package
nl.lumc.sasc.biopet.extensions.gatk
import
java.io.File
import
nl.lumc.sasc.biopet.core.config.Configurable
import
org.broadinstitute.gatk.queue.extensions.gatk.TaggedFile
class
VariantRecalibrator
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
VariantRecalibrator
with
GatkGeneral
{
nt
=
Option
(
getThreads
(
4
))
memoryLimit
=
Option
(
nt
.
getOrElse
(
1
)
*
2
)
if
(
config
.
contains
(
"dbsnp"
))
resource
:+=
new
TaggedFile
(
config
(
"dbsnp"
).
asString
,
"known=true,training=false,truth=false,prior=2.0"
)
an
=
config
(
"annotation"
,
default
=
List
(
"QD"
,
"DP"
,
"FS"
,
"ReadPosRankSum"
,
"MQRankSum"
)).
asStringList
minNumBadVariants
=
config
(
"minnumbadvariants"
)
maxGaussians
=
config
(
"maxgaussians"
)
}
object
VariantRecalibrator
{
def
apply
(
root
:
Configurable
,
input
:
File
,
recal_file
:
File
,
tranches_file
:
File
,
indel
:
Boolean
=
false
)
:
VariantRecalibrator
=
{
val
vr
=
new
VariantRecalibrator
(
root
)
{
override
lazy
val
configName
=
"variantrecalibrator"
override
def
configPath
:
List
[
String
]
=
(
if
(
indel
)
"indel"
else
"snp"
)
::
super
.
configPath
if
(
indel
)
{
mode
=
org
.
broadinstitute
.
gatk
.
tools
.
walkers
.
variantrecalibration
.
VariantRecalibratorArgumentCollection
.
Mode
.
INDEL
defaults
++=
Map
(
"ts_filter_level"
->
99.0
)
if
(
config
.
contains
(
"mills"
))
resource
:+=
new
TaggedFile
(
config
(
"mills"
).
asString
,
"known=false,training=true,truth=true,prior=12.0"
)
}
else
{
mode
=
org
.
broadinstitute
.
gatk
.
tools
.
walkers
.
variantrecalibration
.
VariantRecalibratorArgumentCollection
.
Mode
.
SNP
defaults
++=
Map
(
"ts_filter_level"
->
99.5
)
if
(
config
.
contains
(
"hapmap"
))
resource
+:=
new
TaggedFile
(
config
(
"hapmap"
).
asString
,
"known=false,training=true,truth=true,prior=15.0"
)
if
(
config
.
contains
(
"omni"
))
resource
+:=
new
TaggedFile
(
config
(
"omni"
).
asString
,
"known=false,training=true,truth=true,prior=12.0"
)
if
(
config
.
contains
(
"1000G"
))
resource
+:=
new
TaggedFile
(
config
(
"1000G"
).
asString
,
"known=false,training=true,truth=false,prior=10.0"
)
}
}
vr
.
input
:+=
input
vr
.
recal_file
=
recal_file
vr
.
tranches_file
=
tranches_file
return
vr
}
}
\ No newline at end of file
protected/pom.xml
View file @
6441dfd0
...
...
@@ -8,6 +8,9 @@
</parent>
<artifactId>
protected
</artifactId>
<packaging>
pom
</packaging>
<modules>
<module>
biopet-gatk-extensions
</module>
</modules>
<properties>
<project.build.sourceEncoding>
UTF-8
</project.build.sourceEncoding>
</properties>
...
...
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