diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q index 1ac789f9f..416a5d57a 100755 --- a/scala/qscript/fullCallingPipeline.q +++ b/scala/qscript/fullCallingPipeline.q @@ -1,7 +1,7 @@ import net.sf.picard.reference.FastaSequenceFile 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.{CommandLineGATK, DownsampleType} import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction import org.broadinstitute.sting.queue.extensions.samtools._ @@ -313,6 +313,7 @@ class fullCallingPipeline extends QScript { eval.reportLocation = new File(base+".eval") eval.reportType = Option(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.R) eval.analysisName = base+"_VariantEval" + eval.DBSNP = qscript.pipeline.getProject.getDBSNP add(snps)