htsjdk.samtools
org.broadinstitute.hellbender
org.broadinstitute.hellbender.cmdline
org.broadinstitute.hellbender.cmdline.GATKPlugin
org.broadinstitute.hellbender.cmdline.argumentcollections
org.broadinstitute.hellbender.cmdline.programgroups
org.broadinstitute.hellbender.engine
org.broadinstitute.hellbender.engine.filters
org.broadinstitute.hellbender.engine.spark
org.broadinstitute.hellbender.engine.spark.datasources
org.broadinstitute.hellbender.exceptions
org.broadinstitute.hellbender.metrics
org.broadinstitute.hellbender.metrics.analysis
org.broadinstitute.hellbender.tools
org.broadinstitute.hellbender.tools.copynumber
org.broadinstitute.hellbender.tools.copynumber.arguments
org.broadinstitute.hellbender.tools.copynumber.caller
org.broadinstitute.hellbender.tools.copynumber.datacollection
org.broadinstitute.hellbender.tools.copynumber.denoising
org.broadinstitute.hellbender.tools.copynumber.formats
org.broadinstitute.hellbender.tools.copynumber.formats.collections
org.broadinstitute.hellbender.tools.copynumber.formats.metadata
org.broadinstitute.hellbender.tools.copynumber.formats.records
org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation
org.broadinstitute.hellbender.tools.copynumber.gcnv
org.broadinstitute.hellbender.tools.copynumber.models
org.broadinstitute.hellbender.tools.copynumber.plotting
org.broadinstitute.hellbender.tools.copynumber.segmentation
org.broadinstitute.hellbender.tools.copynumber.utils
org.broadinstitute.hellbender.tools.copynumber.utils.annotatedinterval
org.broadinstitute.hellbender.tools.copynumber.utils.germlinetagging
org.broadinstitute.hellbender.tools.copynumber.utils.optimization
org.broadinstitute.hellbender.tools.copynumber.utils.segmentation
org.broadinstitute.hellbender.tools.examples
org.broadinstitute.hellbender.tools.examples.metrics.multi
org.broadinstitute.hellbender.tools.examples.metrics.single
org.broadinstitute.hellbender.tools.exome
org.broadinstitute.hellbender.tools.exome.orientationbiasvariantfilter
org.broadinstitute.hellbender.tools.funcotator
org.broadinstitute.hellbender.tools.funcotator.compositeoutput
org.broadinstitute.hellbender.tools.funcotator.dataSources
org.broadinstitute.hellbender.tools.funcotator.dataSources.cosmic
org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode
org.broadinstitute.hellbender.tools.funcotator.dataSources.gencode.segment
org.broadinstitute.hellbender.tools.funcotator.dataSources.vcf
org.broadinstitute.hellbender.tools.funcotator.dataSources.xsv
org.broadinstitute.hellbender.tools.funcotator.filtrationRules
org.broadinstitute.hellbender.tools.funcotator.genelistoutput
org.broadinstitute.hellbender.tools.funcotator.mafOutput
org.broadinstitute.hellbender.tools.funcotator.metadata
org.broadinstitute.hellbender.tools.funcotator.simpletsvoutput
org.broadinstitute.hellbender.tools.funcotator.vcfOutput
org.broadinstitute.hellbender.tools.genomicsdb
org.broadinstitute.hellbender.tools.readersplitters
org.broadinstitute.hellbender.tools.spark
org.broadinstitute.hellbender.tools.spark.bwa
org.broadinstitute.hellbender.tools.spark.pathseq
org.broadinstitute.hellbender.tools.spark.pathseq.loggers
org.broadinstitute.hellbender.tools.spark.pipelines
org.broadinstitute.hellbender.tools.spark.pipelines.metrics
org.broadinstitute.hellbender.tools.spark.sv
org.broadinstitute.hellbender.tools.spark.sv.discovery
org.broadinstitute.hellbender.tools.spark.sv.discovery.alignment
org.broadinstitute.hellbender.tools.spark.sv.discovery.inference
org.broadinstitute.hellbender.tools.spark.sv.evidence
org.broadinstitute.hellbender.tools.spark.sv.utils
org.broadinstitute.hellbender.tools.spark.transforms
org.broadinstitute.hellbender.tools.spark.transforms.markduplicates
org.broadinstitute.hellbender.tools.spark.utils
org.broadinstitute.hellbender.tools.spark.validation
org.broadinstitute.hellbender.tools.validation
org.broadinstitute.hellbender.tools.walkers
org.broadinstitute.hellbender.tools.walkers.annotator
org.broadinstitute.hellbender.tools.walkers.annotator.allelespecific
org.broadinstitute.hellbender.tools.walkers.bqsr
org.broadinstitute.hellbender.tools.walkers.contamination
org.broadinstitute.hellbender.tools.walkers.fasta
org.broadinstitute.hellbender.tools.walkers.filters
org.broadinstitute.hellbender.tools.walkers.genotyper
org.broadinstitute.hellbender.tools.walkers.genotyper.afcalc
org.broadinstitute.hellbender.tools.walkers.gnarlyGenotyper
org.broadinstitute.hellbender.tools.walkers.haplotypecaller
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.readthreading
org.broadinstitute.hellbender.tools.walkers.mutect
org.broadinstitute.hellbender.tools.walkers.mutect.clustering
org.broadinstitute.hellbender.tools.walkers.mutect.filtering
org.broadinstitute.hellbender.tools.walkers.qc
org.broadinstitute.hellbender.tools.walkers.readorientation
org.broadinstitute.hellbender.tools.walkers.realignmentfilter
org.broadinstitute.hellbender.tools.walkers.rnaseq
org.broadinstitute.hellbender.tools.walkers.validation
org.broadinstitute.hellbender.tools.walkers.validation.basicshortmutpileup
org.broadinstitute.hellbender.tools.walkers.varianteval
org.broadinstitute.hellbender.tools.walkers.varianteval.evaluators
org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications
org.broadinstitute.hellbender.tools.walkers.varianteval.stratifications.manager
org.broadinstitute.hellbender.tools.walkers.varianteval.util
org.broadinstitute.hellbender.tools.walkers.variantutils
org.broadinstitute.hellbender.tools.walkers.vqsr
org.broadinstitute.hellbender.transformers
org.broadinstitute.hellbender.utils
org.broadinstitute.hellbender.utils.R
org.broadinstitute.hellbender.utils.activityprofile
org.broadinstitute.hellbender.utils.artifacts
org.broadinstitute.hellbender.utils.baq
org.broadinstitute.hellbender.utils.bwa
org.broadinstitute.hellbender.utils.clipping
org.broadinstitute.hellbender.utils.codecs
org.broadinstitute.hellbender.utils.codecs.gencode
org.broadinstitute.hellbender.utils.codecs.sampileup
org.broadinstitute.hellbender.utils.codecs.table
org.broadinstitute.hellbender.utils.codecs.xsvLocatableTable
org.broadinstitute.hellbender.utils.collections
org.broadinstitute.hellbender.utils.config
org.broadinstitute.hellbender.utils.downsampling
org.broadinstitute.hellbender.utils.fasta
org.broadinstitute.hellbender.utils.fragments
org.broadinstitute.hellbender.utils.functional
org.broadinstitute.hellbender.utils.gcs
org.broadinstitute.hellbender.utils.genotyper
org.broadinstitute.hellbender.utils.haplotype
org.broadinstitute.hellbender.utils.help
org.broadinstitute.hellbender.utils.hmm
org.broadinstitute.hellbender.utils.illumina
org.broadinstitute.hellbender.utils.io
org.broadinstitute.hellbender.utils.iterators
org.broadinstitute.hellbender.utils.locusiterator
org.broadinstitute.hellbender.utils.logging
org.broadinstitute.hellbender.utils.mcmc
org.broadinstitute.hellbender.utils.nio
org.broadinstitute.hellbender.utils.pairhmm
org.broadinstitute.hellbender.utils.param
org.broadinstitute.hellbender.utils.pileup
org.broadinstitute.hellbender.utils.python
org.broadinstitute.hellbender.utils.read
org.broadinstitute.hellbender.utils.read.markduplicates
org.broadinstitute.hellbender.utils.read.markduplicates.sparkrecords
org.broadinstitute.hellbender.utils.read.mergealignment
org.broadinstitute.hellbender.utils.recalibration
org.broadinstitute.hellbender.utils.recalibration.covariates
org.broadinstitute.hellbender.utils.reference
org.broadinstitute.hellbender.utils.report
org.broadinstitute.hellbender.utils.runtime
org.broadinstitute.hellbender.utils.samples
org.broadinstitute.hellbender.utils.smithwaterman
org.broadinstitute.hellbender.utils.solver
org.broadinstitute.hellbender.utils.spark
org.broadinstitute.hellbender.utils.svd
org.broadinstitute.hellbender.utils.text
org.broadinstitute.hellbender.utils.tsv
org.broadinstitute.hellbender.utils.variant
org.broadinstitute.hellbender.utils.variant.writers
picard
picard.analysis
picard.analysis.artifacts
picard.analysis.directed
picard.analysis.replicates
picard.annotation
picard.arrays
picard.arrays.illumina
picard.cmdline
picard.cmdline.argumentcollections
picard.cmdline.programgroups
picard.fastq
picard.filter
picard.fingerprint
picard.illumina
picard.illumina.parser
picard.illumina.parser.fakers
picard.illumina.parser.readers
picard.illumina.quality
picard.metrics
picard.nio
picard.pedigree
picard.reference
picard.sam
picard.sam.SamErrorMetric
picard.sam.markduplicates
picard.sam.markduplicates.util
picard.sam.util
picard.util
picard.util.IntervalList
picard.util.help
picard.vcf
picard.vcf.MendelianViolations
picard.vcf.filter
picard.vcf.processor
picard.vcf.processor.util