GenomeAnalysisTK org.broadinstitute.sting.gatk.CommandLineGATK org.broadinstitute.sting.gatk.filters org.broadinstitute.sting.gatk.walkers.CountLociWalker org.broadinstitute.sting.gatk.walkers.CountReadsWalker org.broadinstitute.sting.gatk.walkers.DepthOfCoverageWalker org.broadinstitute.sting.gatk.walkers.PileupWalker org.broadinstitute.sting.gatk.walkers.PrintReadsWalker org.broadinstitute.sting.gatk.walkers.ValidatingPileupWalker org.broadinstitute.sting.gatk.walkers.recalibration.CovariateCounterWalker org.broadinstitute.sting.gatk.walkers.recalibration.TableRecalibrationWalker org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker org.broadinstitute.sting.gatk.walkers.indels.IntervalCleanerWalker org.broadinstitute.sting.gatk.walkers.indels.IntervalMergerWalker org.broadinstitute.sting.gatk.walkers.indels.MismatchIntervalWalker org.broadinstitute.sting.gatk.walkers.indels.SNPClusterWalker org.broadinstitute.sting.playground.gatk.walkers.variants.VariantFiltrationWalker org.broadinstitute.sting.gatk.walkers.genotyper.SingleSampleGenotyper org.broadinstitute.sting.playground.gatk.walkers.variants.IVFSecondaryBases org.broadinstitute.sting.playground.gatk.walkers.variants.VECFisherStrand org.broadinstitute.sting.playground.gatk.walkers.variants.VECAlleleBalance org.broadinstitute.sting.playground.gatk.walkers.variants.VECDepthOfCoverage org.broadinstitute.sting.playground.gatk.walkers.variants.VECLodThreshold org.broadinstitute.sting.playground.gatk.walkers.variants.VECMappingQualityZero org.broadinstitute.sting.playground.gatk.walkers.variants.VECIndelArtifact org.broadinstitute.sting.playground.gatk.walkers.variants.VECClusteredSnps java/src/org/broadinstitute/sting/gatk/walkers/CountReadsWalker.java java/src/org/broadinstitute/sting/gatk/walkers/CountLociWalker.java java/src/org/broadinstitute/sting/gatk/walkers/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/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