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Added a GSA specific package with Playground walkers. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2597 348d0f76-0448-11de-a6fe-93d51630548a
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kshakir 2010-01-15 20:50:29 +00:00
parent 404b95183f
commit 190335db9c
1 changed files with 56 additions and 0 deletions
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packages/GATK-GSA-Pipeline.xml 100644
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<?xml version="1.0" encoding="UTF-8"?>
<!-- NOTE: Uses playground.
ant clean playground package -Dexecutable=GATK-GSA-Pipeline -->
<package>
<name>GATK-GSA-Pipeline</name>
<executable>
<name>GATK-GSA-Pipeline</name>
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
<dependencies>
<package>org.broadinstitute.sting.gatk.filters</package>
<class>org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.PileupWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.PrintReadsWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker</class>
<!-- Quality scores recalibration -->
<class>org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker</class>
<!-- Recalibration Covariates -->
<class>org.broadinstitute.sting.gatk.walkers.recalibration.DinucCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.QualityScoreCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.CycleCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
<class>org.broadinstitute.sting.gatk.walkers.recalibration.HomopolymerCovariate</class>
<!-- Local realignment around indels -->
<class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.SNPClusterWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperWalker</class>
<class>org.broadinstitute.sting.gatk.walkers.indels.IndelGenotyperV2Walker</class>
<!-- Unified genotyper -->
<class>org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyper</class>
<!-- Variant filtration -->
<class>org.broadinstitute.sting.gatk.walkers.filters.VariantFiltrationWalker</class>
<!-- Variant annotator -->
<class>org.broadinstitute.sting.gatk.walkers.annotator.VariantAnnotator</class>
<!-- And the annotations -->
<class>org.broadinstitute.sting.gatk.walkers.annotator.AlleleBalance</class>
<class>org.broadinstitute.sting.gatk.walkers.annotator.DepthOfCoverage</class>
<class>org.broadinstitute.sting.gatk.walkers.annotator.HomopolymerRun</class>
<class>org.broadinstitute.sting.gatk.walkers.annotator.RMSMappingQuality</class>
<class>org.broadinstitute.sting.gatk.walkers.annotator.SpanningDeletions</class>
<!-- From playground -->
<class>org.broadinstitute.sting.playground.gatk.walkers.varianteval.VariantEvalWalker</class>
<class>org.broadinstitute.sting.playground.gatk.walkers.contamination.FindContaminatingReadGroupsWalker</class>
</dependencies>
</executable>
</package>