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Making indel calls default in the MDCP 

You can turn off indel calling by using -noIndels.
This commit is contained in:
Mauricio Carneiro 2011-09-09 14:09:11 -04:00
parent 1953edcd2d
commit 7f9000382e
1 changed files with 3 additions and 3 deletions
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6
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
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@ -22,8 +22,8 @@ class MethodsDevelopmentCallingPipeline extends QScript {
@Argument(shortName="noBAQ", doc="turns off BAQ calculation", required=false) @Argument(shortName="noBAQ", doc="turns off BAQ calculation", required=false)
var noBAQ: Boolean = false var noBAQ: Boolean = false
@Argument(shortName="indels", doc="calls indels with the Unified Genotyper", required=false) @Argument(shortName="noIndels", doc="do not call indels with the Unified Genotyper", required=false)
var callIndels: Boolean = false var noIndels: Boolean = false
@Argument(shortName="LOCAL_ET", doc="Doesn't use the AWS S3 storage for ET option", required=false) @Argument(shortName="LOCAL_ET", doc="Doesn't use the AWS S3 storage for ET option", required=false)
var LOCAL_ET: Boolean = false var LOCAL_ET: Boolean = false
@ -165,7 +165,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
val goldStandard = true val goldStandard = true
for (target <- targets) { for (target <- targets) {
if( !skipCalling ) { if( !skipCalling ) {
if (callIndels) add(new indelCall(target), new indelFilter(target), new indelEvaluation(target)) if (!noIndels) add(new indelCall(target), new indelFilter(target), new indelEvaluation(target))
add(new snpCall(target)) add(new snpCall(target))
add(new VQSR(target, !goldStandard)) add(new VQSR(target, !goldStandard))
add(new applyVQSR(target, !goldStandard)) add(new applyVQSR(target, !goldStandard))