From 7f9000382e4d9ef30e25739401b72e7d1a7c2fcc Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Fri, 9 Sep 2011 14:09:11 -0400 Subject: [PATCH] Making indel calls default in the MDCP You can turn off indel calling by using -noIndels. --- .../queue/qscripts/MethodsDevelopmentCallingPipeline.scala | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala index 80bfe03d1..17d614290 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala @@ -22,8 +22,8 @@ class MethodsDevelopmentCallingPipeline extends QScript { @Argument(shortName="noBAQ", doc="turns off BAQ calculation", required=false) var noBAQ: Boolean = false - @Argument(shortName="indels", doc="calls indels with the Unified Genotyper", required=false) - var callIndels: Boolean = false + @Argument(shortName="noIndels", doc="do not call indels with the Unified Genotyper", required=false) + var noIndels: Boolean = false @Argument(shortName="LOCAL_ET", doc="Doesn't use the AWS S3 storage for ET option", required=false) var LOCAL_ET: Boolean = false @@ -165,7 +165,7 @@ class MethodsDevelopmentCallingPipeline extends QScript { val goldStandard = true for (target <- targets) { 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 VQSR(target, !goldStandard)) add(new applyVQSR(target, !goldStandard))