diff --git a/packages/GATK-GSA-Pipeline.xml b/packages/GATK-GSA-Pipeline.xml new file mode 100644 index 000000000..77fb6025c --- /dev/null +++ b/packages/GATK-GSA-Pipeline.xml @@ -0,0 +1,56 @@ + + + + GATK-GSA-Pipeline + + GATK-GSA-Pipeline + org.broadinstitute.sting.gatk.CommandLineGATK + + org.broadinstitute.sting.gatk.filters + org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker + org.broadinstitute.sting.gatk.walkers.PileupWalker + org.broadinstitute.sting.gatk.walkers.PrintReadsWalker + org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker + org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker + org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker + + org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker + org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker + + org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate + org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate + org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate + org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate + org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate + org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate + org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate + org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate + org.broadinstitute.sting.gatk.walkers.recalibration.HomopolymerCovariate + + org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector + org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker + org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker + org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker + org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker + org.broadinstitute.sting.gatk.walkers.indels.SNPClusterWalker + org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperWalker + org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperV2Walker + + org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper + + org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker + + org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator + + org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance + org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage + org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun + org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality + org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions + + org.broadinstitute.sting.playground.gatk.walkers.varianteval.VariantEvalWalker + org.broadinstitute.sting.playground.gatk.walkers.contamination.FindContaminatingReadGroupsWalker + + +