diff --git a/packages/GATK-Picard.xml b/packages/GATK-Picard.xml new file mode 100644 index 000000000..c830b60d2 --- /dev/null +++ b/packages/GATK-Picard.xml @@ -0,0 +1,88 @@ + + + GATK-Picard + + GATK-Picard + org.broadinstitute.sting.gatk.CommandLineGATK + + org.broadinstitute.sting.gatk.filters + org.broadinstitute.sting.gatk.walkers.CountLociWalker + org.broadinstitute.sting.gatk.walkers.CountReadsWalker + 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.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.TileCovariate + + 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.MappingQualityZero + org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality + org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions + + + + AnalyzeCovariates + org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates + + + org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates + 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 + + + + + java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java + java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java + java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java + java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java + java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java + java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java + java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java + java/src/org/broadinstitute/sting/gatk/examples/build.xml + + testdata/exampleBAM.bam + testdata/exampleBAM.bam.bai + testdata/exampleFASTA.fasta + testdata/exampleFASTA.fasta.fai + testdata/exampleFASTA.dict + + R/plot_residualError_OtherCovariate.R + R/plot_residualError_QualityScoreCovariate.R + +