73 lines
4.6 KiB
XML
73 lines
4.6 KiB
XML
<?xml version="1.0" encoding="UTF-8"?>
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<package>
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<name>GenomeAnalysisTK</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.CountLociWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.CountReadsWalker</class>
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<class>org.broadinstitute.sting.gatk.walkers.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.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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<!-- 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.FisherStrand</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.MappingQualityZero</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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</dependencies>
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<resources>
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<!-- GATK sample code and build scripts -->
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<file>java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java</file>
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<file>java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java</file>
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<file>java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java</file>
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<file>java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java</file>
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<file>java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java</file>
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<file>java/src/org/broadinstitute/sting/gatk/walkers/ValidatingPileupWalker.java</file>
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<file>java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java</file>
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<file>java/src/org/broadinstitute/sting/gatk/examples/build.xml</file>
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<!-- Sample reads and reference files -->
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<file>testdata/exampleBAM.bam</file>
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<file>testdata/exampleBAM.bam.bai</file>
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<file>testdata/exampleFASTA.fasta</file>
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<file>testdata/exampleFASTA.fasta.fai</file>
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<file>testdata/exampleFASTA.dict</file>
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<!-- Supplemental scripts for graph generation, etc. -->
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<file>python/analyzeRecalQuals_1KG.py</file>
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<file>testdata/recalConfig_1KG.cfg</file>
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<file>R/plot_q_emp_stated_hst.R</file>
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<file>R/plot_qual_diff_v_cycle.R</file>
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<file>R/plot_qual_diff_v_dinuc.R</file>
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</resources>
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</package>
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