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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
This commit is contained in:
chartl 2010-08-31 15:21:41 +00:00
parent 3c956110f3
commit 1a14dbee1e
1 changed files with 6 additions and 1 deletions
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7
scala/qscript/fullCallingPipeline.q
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@ -1,6 +1,7 @@
import org.broadinstitute.sting.gatk.DownsampleType import org.broadinstitute.sting.gatk.DownsampleType
import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeCalculationModel.Model import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeCalculationModel.Model
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.samtools._
import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.QScript
class fullCallingPipeline extends QScript { class fullCallingPipeline extends QScript {
@ -70,6 +71,7 @@ class fullCallingPipeline extends QScript {
this.reference_sequence = qscript.reference this.reference_sequence = qscript.reference
} }
// ------------ SETUP THE PIPELINE ----------- // // ------------ SETUP THE PIPELINE ----------- //
@ -105,11 +107,14 @@ class fullCallingPipeline extends QScript {
realigner.setupGatherFunction = { case (f: BamGatherFunction, _) => f.jarFile = qscript.picardFixMatesJar } realigner.setupGatherFunction = { case (f: BamGatherFunction, _) => f.jarFile = qscript.picardFixMatesJar }
realigner.jobQueue = "week" realigner.jobQueue = "week"
var samtoolsindex = new SamtoolsIndexFunction
samtoolsindex.bamFile = cleaned_bam
// put clean bams in clean genotypers // put clean bams in clean genotypers
cleanBamFiles :+= realigner.out.toNamedFile cleanBamFiles :+= realigner.out.toNamedFile
add(targetCreator,realigner) add(targetCreator,realigner,samtoolsindex)
} }
// actually make calls // actually make calls