GATK-Picard GATK-Picard org.broadinstitute.sting.gatk.CommandLineGATK StingText.properties QualityScoresRecalibrationModule.xml LocalRealignmentAroundIndelsModule.xml UnifiedGenotyperModule.xml VariantFiltrationModule.xml VariantAnnotatorModule.xml org.broadinstitute.sting.gatk.filters org.broadinstitute.sting.gatk.walkers.coverage.DepthOfCoverageWalker org.broadinstitute.sting.gatk.walkers.PileupWalker org.broadinstitute.sting.gatk.walkers.PrintReadsWalker org.broadinstitute.sting.gatk.walkers.qc.CountLociWalker org.broadinstitute.sting.gatk.walkers.qc.CountReadsWalker org.broadinstitute.sting.gatk.walkers.qc.ValidatingPileupWalker org.broadinstitute.sting.gatk.walkers.recalibration.PositionCovariate org.broadinstitute.sting.gatk.walkers.recalibration.MinimumNQSCovariate org.broadinstitute.sting.gatk.walkers.recalibration.MappingQualityCovariate org.broadinstitute.sting.gatk.walkers.recalibration.PrimerRoundCovariate org.broadinstitute.sting.gatk.walkers.recalibration.HomopolymerCovariate java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java java/src/org/broadinstitute/sting/gatk/walkers/PileupWalker.java java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java java/src/org/broadinstitute/sting/gatk/walkers/qc/CountLociWalker.java java/src/org/broadinstitute/sting/gatk/walkers/qc/CountReadsWalker.java java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java java/src/org/broadinstitute/sting/gatk/examples/HelloWalker.java java/src/org/broadinstitute/sting/gatk/examples/build.xml testdata/exampleBAM.bam testdata/exampleBAM.bam.bai testdata/exampleFASTA.fasta testdata/exampleFASTA.fasta.fai testdata/exampleFASTA.dict R/plot_residualError_OtherCovariate.R R/plot_residualError_QualityScoreCovariate.R