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biopet.biopet
Commits
90e81770
Commit
90e81770
authored
Feb 03, 2017
by
Peter van 't Hof
Browse files
Only show argument at gatk 3.6 or lower
parent
cefa43a5
Changes
2
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
View file @
90e81770
...
...
@@ -453,7 +453,6 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
optional
(
"-hets"
,
heterozygosity
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
heterozygosityFormat
)
+
optional
(
"-indelHeterozygosity"
,
indel_heterozygosity
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
indel_heterozygosityFormat
)
+
optional
(
"-stand_call_conf"
,
standard_min_confidence_threshold_for_calling
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
standard_min_confidence_threshold_for_callingFormat
)
+
optional
(
"-stand_emit_conf"
,
standard_min_confidence_threshold_for_emitting
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
standard_min_confidence_threshold_for_emittingFormat
)
+
optional
(
"-maxAltAlleles"
,
max_alternate_alleles
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-inputPrior"
,
input_prior
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-ploidy"
,
sample_ploidy
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
...
...
@@ -512,7 +511,12 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
optional
(
"-mmq"
,
min_mapping_quality_score
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
filter_reads_with_N_cigar
,
"-filterRNC"
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
filter_mismatching_base_and_quals
,
"-filterMBQ"
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
filter_bases_not_stored
,
"-filterNoBases"
,
escape
=
true
,
format
=
"%s"
)
conditional
(
filter_bases_not_stored
,
"-filterNoBases"
,
escape
=
true
,
format
=
"%s"
)
+
(
this
.
getVersion
match
{
case
Some
(
s
)
if
s
.
contains
(
"3.0"
)
|
s
.
contains
(
"3.1"
)
|
s
.
contains
(
"3.2"
)
|
s
.
contains
(
"3.3"
)
|
s
.
contains
(
"3.4"
)
|
s
.
contains
(
"3.5"
)
|
s
.
contains
(
"3.6"
)
=>
optional
(
"-stand_emit_conf"
,
standard_min_confidence_threshold_for_emitting
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
standard_min_confidence_threshold_for_emittingFormat
)
case
_
=>
""
})
}
object
HaplotypeCaller
{
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
View file @
90e81770
...
...
@@ -300,7 +300,6 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
optional
(
"-hets"
,
heterozygosity
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
heterozygosityFormat
)
+
optional
(
"-indelHeterozygosity"
,
indel_heterozygosity
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
indel_heterozygosityFormat
)
+
optional
(
"-stand_call_conf"
,
standard_min_confidence_threshold_for_calling
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
standard_min_confidence_threshold_for_callingFormat
)
+
optional
(
"-stand_emit_conf"
,
standard_min_confidence_threshold_for_emitting
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
standard_min_confidence_threshold_for_emittingFormat
)
+
optional
(
"-maxAltAlleles"
,
max_alternate_alleles
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
repeat
(
"-inputPrior"
,
input_prior
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
optional
(
"-ploidy"
,
sample_ploidy
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
...
...
@@ -323,7 +322,12 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
repeat
(
"-G"
,
group
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
filter_reads_with_N_cigar
,
"-filterRNC"
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
filter_mismatching_base_and_quals
,
"-filterMBQ"
,
escape
=
true
,
format
=
"%s"
)
+
conditional
(
filter_bases_not_stored
,
"-filterNoBases"
,
escape
=
true
,
format
=
"%s"
)
conditional
(
filter_bases_not_stored
,
"-filterNoBases"
,
escape
=
true
,
format
=
"%s"
)
+
(
this
.
getVersion
match
{
case
Some
(
s
)
if
s
.
contains
(
"3.0"
)
|
s
.
contains
(
"3.1"
)
|
s
.
contains
(
"3.2"
)
|
s
.
contains
(
"3.3"
)
|
s
.
contains
(
"3.4"
)
|
s
.
contains
(
"3.5"
)
|
s
.
contains
(
"3.6"
)
=>
optional
(
"-stand_emit_conf"
,
standard_min_confidence_threshold_for_emitting
,
spaceSeparated
=
true
,
escape
=
true
,
format
=
standard_min_confidence_threshold_for_emittingFormat
)
case
_
=>
""
})
}
object
UnifiedGenotyper
{
...
...
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