Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
B
biopet.biopet
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Operations
Operations
Environments
Analytics
Analytics
CI / CD
Repository
Value Stream
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Jobs
Commits
Open sidebar
Mirrors
biopet.biopet
Commits
3babdbc3
Commit
3babdbc3
authored
Jan 08, 2016
by
Wai Yi Leung
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Merging SV calls - changed post-calling step in several SV-callers
parent
6f59dc48
Changes
5
Hide whitespace changes
Inline
Side-by-side
Showing
5 changed files
with
29 additions
and
12 deletions
+29
-12
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala
...main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala
+7
-9
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
.../nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
+16
-2
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
...c/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
+2
-0
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
...l/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
+2
-0
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
...nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
+2
-1
No files found.
public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Pysvtools.scala
View file @
3babdbc3
...
...
@@ -8,20 +8,19 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline._
/**
* Created by wyleung on 8-1-16.
*/
* Created by wyleung on 8-1-16.
*/
class
Pysvtools
(
val
root
:
Configurable
)
extends
BiopetCommandLineFunction
{
@Input
(
doc
=
"Input file"
,
required
=
true
)
var
input
:
List
[
File
]
=
Nil
@Argument
(
doc
=
"Set flanking amount"
)
@Argument
(
doc
=
"Set flanking amount"
)
var
flanking
:
Option
[
Int
]
=
config
(
"flanking"
)
var
exclusionRegions
:
List
[
File
]
=
config
(
"exclusion_regions"
)
var
translocationsOnly
:
Boolean
=
config
(
"translocations_only"
)
@Output
(
doc
=
"Unzipped file"
,
required
=
true
)
var
output
:
File
=
_
...
...
@@ -43,16 +42,15 @@ class Pysvtools(val root: Configurable) extends BiopetCommandLineFunction {
// redefine the tsv, bed and regions output
val
outputNamePrefix
=
output
.
getAbsolutePath
.
stripSuffix
(
".vcf"
)
tsvoutput
=
new
File
(
outputNamePrefix
+
".tsv"
)
bedoutput
=
new
File
(
outputNamePrefix
+
".bed"
)
regionsoutput
=
new
File
(
outputNamePrefix
+
".regions.bed"
)
tsvoutput
=
new
File
(
outputNamePrefix
+
".tsv"
)
bedoutput
=
new
File
(
outputNamePrefix
+
".bed"
)
regionsoutput
=
new
File
(
outputNamePrefix
+
".regions.bed"
)
}
/** return commandline to execute */
def
cmdLine
=
required
(
executable
)
+
repeat
(
"-c"
,
input
)
+
optional
(
"-f"
,
flanking
)
+
optional
(
"-f"
,
flanking
)
+
"-i "
+
repeat
(
input
)
+
"-o "
+
required
(
tsvoutput
)
+
"-b "
+
required
(
bedoutput
)
+
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCalling.scala
View file @
3babdbc3
...
...
@@ -17,9 +17,10 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import
nl.lumc.sasc.biopet.core.summary.SummaryQScript
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
Reference
,
SampleLibraryTag
}
import
nl.lumc.sasc.biopet.
pipelines.shiva.svcallers.
{
Delly
,
Breakdancer
,
Clever
,
SvCaller
}
import
nl.lumc.sasc.biopet.
utils.
{
BamUtils
,
Logging
}
import
nl.lumc.sasc.biopet.
extensions.Pysvtools
import
nl.lumc.sasc.biopet.
pipelines.shiva.svcallers.
{
Breakdancer
,
Clever
,
Delly
,
SvCaller
}
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.utils.
{
BamUtils
,
Logging
}
import
org.broadinstitute.gatk.queue.QScript
/**
...
...
@@ -62,6 +63,19 @@ class ShivaSvCalling(val root: Configurable) extends QScript with SummaryQScript
add
(
caller
)
}
// merge VCF by sample
for
((
sample
,
bamFile
)
<-
inputBams
)
{
var
sampleVcfs
:
List
[
File
]
=
List
()
callers
.
foreach
{
caller
=>
sampleVcfs
:+=
caller
.
outputFiles
(
sample
)
}
val
mergeSVcalls
=
new
Pysvtools
(
this
)
mergeSVcalls
.
input
=
sampleVcfs
mergeSVcalls
.
output
=
new
File
(
outputDir
,
sample
+
".merged.vcf"
)
add
(
mergeSVcalls
)
outputFiles
+=
(
sample
->
mergeSVcalls
.
output
)
}
addSummaryJobs
()
}
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Breakdancer.scala
View file @
3babdbc3
...
...
@@ -18,6 +18,8 @@ class Breakdancer(val root: Configurable) extends SvCaller {
val
breakdancer
=
BreakdancerCaller
(
this
,
bdcfg
.
output
,
new
File
(
breakdancerSampleDir
,
sample
+
".breakdancer.tsv"
))
val
bdvcf
=
BreakdancerVCF
(
this
,
breakdancer
.
output
,
new
File
(
breakdancerSampleDir
,
sample
+
".breakdancer.vcf"
))
add
(
bdcfg
,
breakdancer
,
bdvcf
)
outputFiles
+=
(
sample
->
bdvcf
.
output
)
}
}
}
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Clever.scala
View file @
3babdbc3
...
...
@@ -13,6 +13,8 @@ class Clever(val root: Configurable) extends SvCaller {
val
cleverDir
=
new
File
(
outputDir
,
sample
)
val
clever
=
CleverCaller
(
this
,
bamFile
,
cleverDir
)
add
(
clever
)
outputFiles
+=
(
sample
->
clever
.
outputvcf
)
}
}
}
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/svcallers/Delly.scala
View file @
3babdbc3
...
...
@@ -20,7 +20,6 @@ class Delly(val root: Configurable) extends SvCaller {
val
catVariants
=
new
CatVariants
(
this
)
catVariants
.
outputFile
=
new
File
(
dellyDir
,
sample
+
".delly.vcf.gz"
)
/// start delly and then copy the vcf into the root directory "<sample>.delly/"
if
(
del
)
{
val
delly
=
new
DellyCaller
(
this
)
delly
.
input
=
bamFile
...
...
@@ -55,6 +54,8 @@ class Delly(val root: Configurable) extends SvCaller {
}
add
(
catVariants
)
outputFiles
+=
(
sample
->
catVariants
.
outputFile
)
}
}
}
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a 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