From 1a14dbee1e5bdb0eabe773343d3f2045efa899bc Mon Sep 17 00:00:00 2001 From: chartl Date: Tue, 31 Aug 2010 15:21:41 +0000 Subject: [PATCH] Adding in .bam indexing; commit for Khalid git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4169 348d0f76-0448-11de-a6fe-93d51630548a --- scala/qscript/fullCallingPipeline.q | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q index 870cc060b..631ec1576 100755 --- a/scala/qscript/fullCallingPipeline.q +++ b/scala/qscript/fullCallingPipeline.q @@ -1,6 +1,7 @@ import org.broadinstitute.sting.gatk.DownsampleType import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeCalculationModel.Model import org.broadinstitute.sting.queue.extensions.gatk._ +import org.broadinstitute.sting.queue.extensions.samtools._ import org.broadinstitute.sting.queue.QScript class fullCallingPipeline extends QScript { @@ -70,6 +71,7 @@ class fullCallingPipeline extends QScript { this.reference_sequence = qscript.reference } + // ------------ SETUP THE PIPELINE ----------- // @@ -105,11 +107,14 @@ class fullCallingPipeline extends QScript { realigner.setupGatherFunction = { case (f: BamGatherFunction, _) => f.jarFile = qscript.picardFixMatesJar } realigner.jobQueue = "week" + var samtoolsindex = new SamtoolsIndexFunction + samtoolsindex.bamFile = cleaned_bam + // put clean bams in clean genotypers cleanBamFiles :+= realigner.out.toNamedFile - add(targetCreator,realigner) + add(targetCreator,realigner,samtoolsindex) } // actually make calls