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Added support python and R scripts for generating covariate output graphs. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1625 348d0f76-0448-11de-a6fe-93d51630548a
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hanna 2009-09-15 14:17:36 +00:00
parent b401929e41
commit e6827424b9
1 changed files with 11 additions and 0 deletions
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11
packages/GenomeAnalysisTK.xml
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@ -35,6 +35,7 @@
<class>org.broadinstitute.sting.playground.gatk.walkers.variants.VECClusteredSnps</class>
</dependencies>
<resources>
<!-- GATK sample code and build scripts -->
<file>java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java</file>
<file>java/src/org/broadinstitute/sting/gatk/walkers/DepthOfCoverageWalker.java</file>
@ -43,10 +44,20 @@
<file>java/src/org/broadinstitute/sting/gatk/walkers/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>python/analyzeRecalQuals.py</file>
<file>python/analyzeRecalQuals_1KG.py</file>
<file>testdata/defaultGATKConfig.cfg</file>
<file>testdata/recalConfig_1KG.cfg</file>
<file>R/logistic_regression.R</file>
<file>R/plot_q_emp_stated_hst.R</file>
<file>R/plot_qual_diff_v_cycle.R</file>
<file>R/plot_qual_diff_v_dinuc.R</file>
</resources>
</package>