53 lines
2.6 KiB
XML
53 lines
2.6 KiB
XML
<?xml version="1.0" encoding="UTF-8"?>
|
|
<package>
|
|
<name>GenomeAnalysisTK</name>
|
|
<version file="StingText.properties" property="org.broadinstitute.sting.gatk.version" />
|
|
<executable>
|
|
<name>GenomeAnalysisTK</name>
|
|
<main-class>org.broadinstitute.sting.gatk.CommandLineGATK</main-class>
|
|
<resource-bundle>StingText.properties</resource-bundle>
|
|
<modules>
|
|
<module>QualityScoresRecalibration.xml</module>
|
|
<module>LocalRealignmentAroundIndels.xml</module>
|
|
<module>UnifiedGenotyper.xml</module>
|
|
<module>VariantFiltration.xml</module>
|
|
<module>VariantAnnotator.xml</module>
|
|
<module>VCFValidator.xml</module>
|
|
</modules>
|
|
<dependencies>
|
|
<!-- Filters -->
|
|
<package>org.broadinstitute.sting.gatk.filters</package>
|
|
<!-- Basic qc walkers -->
|
|
<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>
|
|
</dependencies>
|
|
</executable>
|
|
<modules>
|
|
<module>AnalyzeCovariates.xml</module>
|
|
</modules>
|
|
<resources>
|
|
<!-- GATK sample code and build scripts -->
|
|
<file>java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java</file>
|
|
<file>java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java</file>
|
|
<file>java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java</file>
|
|
<file>java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java</file>
|
|
<file>java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java</file>
|
|
<file>java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java</file>
|
|
<file>java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java</file>
|
|
<file>java/src/org/broadinstitute/sting/gatk/examples/build.xml</file>
|
|
<!-- Sample reads and reference files -->
|
|
<file>testdata/exampleBAM.bam</file>
|
|
<file>testdata/exampleBAM.bam.bai</file>
|
|
<file>testdata/exampleFASTA.fasta</file>
|
|
<file>testdata/exampleFASTA.fasta.fai</file>
|
|
<file>testdata/exampleFASTA.dict</file>
|
|
<!-- Supplemental scripts for graph generation, etc. -->
|
|
<file>R/plot_residualError_OtherCovariate.R</file>
|
|
<file>R/plot_residualError_QualityScoreCovariate.R</file>
|
|
</resources>
|
|
</package>
|