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
55629dcb
Commit
55629dcb
authored
Nov 30, 2015
by
Peter van 't Hof
Browse files
Fixed vcf index files
parent
0929d425
Changes
5
Hide whitespace changes
Inline
Side-by-side
protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
View file @
55629dcb
...
...
@@ -5,9 +5,17 @@
*/
package
nl.lumc.sasc.biopet.extensions.gatk.broad
import
java.io.File
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.Output
class
UnifiedGenotyper
(
val
root
:
Configurable
)
extends
org
.
broadinstitute
.
gatk
.
queue
.
extensions
.
gatk
.
UnifiedGenotyper
with
GatkGeneral
{
@Output
(
required
=
false
)
protected
var
vcfIndex
:
File
=
_
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
if
(
config
.
contains
(
"dbsnp"
))
this
.
dbsnp
=
config
(
"dbsnp"
)
sample_ploidy
=
config
(
"ploidy"
)
...
...
@@ -36,3 +44,14 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
memoryLimit
=
Option
(
nct
.
getOrElse
(
1
)
*
memoryLimit
.
getOrElse
(
2.0
))
}
}
object
UnifiedGenotyper
{
def
apply
(
root
:
Configurable
,
inputFiles
:
List
[
File
],
outputFile
:
File
)
:
UnifiedGenotyper
=
{
val
ug
=
new
UnifiedGenotyper
(
root
)
ug
.
input_file
=
inputFiles
ug
.
out
=
outputFile
if
(
ug
.
out
.
getName
.
endsWith
(
".vcf.gz"
))
ug
.
vcfIndex
=
new
File
(
ug
.
out
.
getAbsolutePath
+
".tbi"
)
ug
}
}
\ No newline at end of file
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/UnifiedGenotyper.scala
View file @
55629dcb
...
...
@@ -2,6 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk.variantcallers
import
nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.broad
/** Default mode for UnifiedGenotyper */
class
UnifiedGenotyper
(
val
root
:
Configurable
)
extends
Variantcaller
{
...
...
@@ -9,9 +10,7 @@ class UnifiedGenotyper(val root: Configurable) extends Variantcaller {
protected
def
defaultPrio
=
20
def
biopetScript
()
{
val
ug
=
new
nl
.
lumc
.
sasc
.
biopet
.
extensions
.
gatk
.
broad
.
UnifiedGenotyper
(
this
)
ug
.
input_file
=
inputBams
.
values
.
toList
ug
.
out
=
outputFile
val
ug
=
broad
.
UnifiedGenotyper
(
this
,
inputBams
.
values
.
toList
,
outputFile
)
add
(
ug
)
}
}
protected/biopet-gatk-pipelines/src/main/scala/nl/lumc/sasc/biopet/pipelines/gatk/variantcallers/UnifiedGenotyperAllele.scala
View file @
55629dcb
...
...
@@ -2,6 +2,7 @@ package nl.lumc.sasc.biopet.pipelines.gatk.variantcallers
import
nl.lumc.sasc.biopet.pipelines.shiva.variantcallers.Variantcaller
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.extensions.gatk.broad
/** Allele mode for GenotyperAllele */
class
UnifiedGenotyperAllele
(
val
root
:
Configurable
)
extends
Variantcaller
{
...
...
@@ -9,9 +10,7 @@ class UnifiedGenotyperAllele(val root: Configurable) extends Variantcaller {
protected
def
defaultPrio
=
9
def
biopetScript
()
{
val
ug
=
new
nl
.
lumc
.
sasc
.
biopet
.
extensions
.
gatk
.
broad
.
UnifiedGenotyper
(
this
)
ug
.
input_file
=
inputBams
.
values
.
toList
ug
.
out
=
outputFile
val
ug
=
broad
.
UnifiedGenotyper
(
this
,
inputBams
.
values
.
toList
,
outputFile
)
ug
.
alleles
=
config
(
"input_alleles"
)
ug
.
genotyping_mode
=
org
.
broadinstitute
.
gatk
.
tools
.
walkers
.
genotyper
.
GenotypingOutputMode
.
GENOTYPE_GIVEN_ALLELES
add
(
ug
)
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/MpileupToVcf.scala
View file @
55629dcb
...
...
@@ -38,6 +38,9 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFunction with Refe
@Output
(
doc
=
"Output tag library"
,
shortName
=
"output"
,
required
=
true
)
var
output
:
File
=
_
@Output
private
var
outputIndex
:
File
=
_
var
minDP
:
Option
[
Int
]
=
config
(
"min_dp"
)
var
minAP
:
Option
[
Int
]
=
config
(
"min_ap"
)
var
homoFraction
:
Option
[
Double
]
=
config
(
"homoFraction"
)
...
...
@@ -50,6 +53,7 @@ class MpileupToVcf(val root: Configurable) extends ToolCommandFunction with Refe
override
def
beforeGraph
()
{
super
.
beforeGraph
()
if
(
reference
==
null
)
reference
=
referenceFasta
().
getAbsolutePath
if
(
output
.
getName
.
endsWith
(
".vcf.gz"
))
outputIndex
=
new
File
(
output
.
getAbsolutePath
+
".tbi"
)
val
samtoolsMpileup
=
new
SamtoolsMpileup
(
this
)
}
...
...
public/biopet-tools-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/tools/VcfFilter.scala
View file @
55629dcb
...
...
@@ -30,6 +30,9 @@ class VcfFilter(val root: Configurable) extends ToolCommandFunction {
@Output
(
doc
=
"Output vcf"
,
shortName
=
"o"
,
required
=
false
)
var
outputVcf
:
File
=
_
@Output
var
outputVcfIndex
:
File
=
_
var
minSampleDepth
:
Option
[
Int
]
=
config
(
"min_sample_depth"
)
var
minTotalDepth
:
Option
[
Int
]
=
config
(
"min_total_depth"
)
var
minAlternateDepth
:
Option
[
Int
]
=
config
(
"min_alternate_depth"
)
...
...
@@ -38,6 +41,11 @@ class VcfFilter(val root: Configurable) extends ToolCommandFunction {
override
def
defaultCoreMemory
=
3.0
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
if
(
outputVcf
.
getName
.
endsWith
(
"vcf.gz"
))
outputVcfIndex
=
new
File
(
outputVcf
.
getAbsolutePath
+
".tbi"
)
}
override
def
cmdLine
=
super
.
cmdLine
+
required
(
"-I"
,
inputVcf
)
+
required
(
"-o"
,
outputVcf
)
+
...
...
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