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Added DbSnp to VariantEval 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4497 348d0f76-0448-11de-a6fe-93d51630548a
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corin 2010-10-14 17:02:17 +00:00
parent 63e3848187
commit 5e0c4ecc21
1 changed files with 2 additions and 1 deletions
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3
scala/qscript/fullCallingPipeline.q
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@ -1,7 +1,7 @@
import net.sf.picard.reference.FastaSequenceFile import net.sf.picard.reference.FastaSequenceFile
import org.broadinstitute.sting.datasources.pipeline.Pipeline import org.broadinstitute.sting.datasources.pipeline.Pipeline
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.gatk.{CommandLineGATK, DownsampleType}
import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.gatk._
import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
import org.broadinstitute.sting.queue.extensions.samtools._ import org.broadinstitute.sting.queue.extensions.samtools._
@ -313,6 +313,7 @@ class fullCallingPipeline extends QScript {
eval.reportLocation = new File(base+".eval") eval.reportLocation = new File(base+".eval")
eval.reportType = Option(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.R) eval.reportType = Option(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.R)
eval.analysisName = base+"_VariantEval" eval.analysisName = base+"_VariantEval"
eval.DBSNP = qscript.pipeline.getProject.getDBSNP
add(snps) add(snps)