58 lines
3.8 KiB
XML
58 lines
3.8 KiB
XML
<?xml version="1.0" encoding="UTF-8"?>
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<!-- NOTE: Uses playground.
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ant clean playground package -Dexecutable=GATK-GSA-Pipeline -->
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<package>
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<name>GATK-GSA-Pipeline</name>
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<executable>
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<name>GATK-GSA-Pipeline</name>
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<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
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<dependencies>
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<package>org.broadinstitute.sting.gatk.filters</package>
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<class>org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker</class>
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<!-- Quality scores recalibration -->
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker</class>
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<!-- Recalibration Covariates -->
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.HomopolymerCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate</class>
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<!-- Local realignment around indels -->
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<class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.SNPClusterWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperV2Walker</class>
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<!-- Unified genotyper -->
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<class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class>
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<!-- Variant filtration -->
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<class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class>
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<!-- Variant annotator -->
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<class>org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator</class>
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<!-- And the annotations -->
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<class>org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality</class>
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<class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</class>
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<!-- From playground -->
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<class>org.broadinstitute.sting.playground.gatk.walkers.varianteval.VariantEvalWalker</class>
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<class>org.broadinstitute.sting.playground.gatk.walkers.contamination.FindContaminatingReadGroupsWalker</class>
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</dependencies>
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</executable>
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</package>
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