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biopet.biopet
Commits
4c3c746b
Commit
4c3c746b
authored
Jun 02, 2016
by
bow
Browse files
Merge branch 'fix-haplotypercaller' into 'develop'
fixed a config value See merge request !417
parents
baa5ab44
a50e42cc
Changes
2
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
View file @
4c3c746b
...
...
@@ -90,7 +90,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
/** Mode for emitting reference confidence scores */
@Argument
(
fullName
=
"emitRefConfidence"
,
shortName
=
"ERC"
,
doc
=
"Mode for emitting reference confidence scores"
,
required
=
false
,
exclusiveOf
=
""
,
validation
=
""
)
var
emitRefConfidence
:
String
=
_
var
emitRefConfidence
:
Option
[
String
]
=
config
(
"emitRefConfidence"
)
/** File to which assembled haplotypes should be written */
@Output
(
fullName
=
"bamOutput"
,
shortName
=
"bamout"
,
doc
=
"File to which assembled haplotypes should be written"
,
required
=
false
,
exclusiveOf
=
""
,
validation
=
""
)
...
...
@@ -522,12 +522,4 @@ object HaplotypeCaller {
hc
.
out
=
outputFile
hc
}
def
gvcf
(
root
:
Configurable
,
inputFile
:
File
,
outputFile
:
File
)
:
HaplotypeCaller
=
{
val
hc
=
apply
(
root
,
List
(
inputFile
),
outputFile
)
hc
.
emitRefConfidence
=
"GVCF"
hc
.
variant_index_type
=
Some
(
"LINEAR"
)
hc
.
variant_index_parameter
=
Some
(
hc
.
config
(
"variant_index_parameter"
,
default
=
128000
).
asInt
)
hc
}
}
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/HaplotypeCallerGvcf.scala
View file @
4c3c746b
...
...
@@ -34,9 +34,16 @@ class HaplotypeCallerGvcf(val root: Configurable) extends Variantcaller {
def
getGvcfs
=
gVcfFiles
override
def
fixedValues
=
Map
(
"haplotypecaller"
->
Map
(
"emitRefConfidence"
->
"GVCF"
))
override
def
defaults
=
Map
(
"haplotypecaller"
->
Map
(
"variant_index_type"
->
"LINEAR"
,
"variant_index_parameter"
->
128000
)
)
def
biopetScript
()
{
val
gvcfFiles
=
for
((
sample
,
inputBam
)
<-
inputBams
)
yield
{
val
hc
=
gatk
.
HaplotypeCaller
.
gvcf
(
this
,
inputBam
,
new
File
(
outputDir
,
sample
+
".gvcf.vcf.gz"
))
val
hc
=
gatk
.
HaplotypeCaller
(
this
,
List
(
inputBam
)
,
new
File
(
outputDir
,
sample
+
".gvcf.vcf.gz"
))
add
(
hc
)
sample
->
hc
.
out
}
...
...
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