gatk 4.4.0.0 API

Packages

Package	Description
htsjdk.samtools
org.broadinstitute.hellbender
org.broadinstitute.hellbender.cmdline
org.broadinstitute.hellbender.cmdline.argumentcollections
org.broadinstitute.hellbender.cmdline.GATKPlugin
org.broadinstitute.hellbender.cmdline.programgroups
org.broadinstitute.hellbender.engine
org.broadinstitute.hellbender.engine.filters
org.broadinstitute.hellbender.engine.filters.flow
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.testutils
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.genotyping
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.dragstr
org.broadinstitute.hellbender.tools.examples
org.broadinstitute.hellbender.tools.examples.metrics.multi
org.broadinstitute.hellbender.tools.examples.metrics.single
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.htsgetreader
org.broadinstitute.hellbender.tools.readersplitters
org.broadinstitute.hellbender.tools.reference
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.sv
org.broadinstitute.hellbender.tools.sv.cluster
org.broadinstitute.hellbender.tools.sv.concordance
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.annotator.flow
org.broadinstitute.hellbender.tools.walkers.bqsr
org.broadinstitute.hellbender.tools.walkers.consensus
org.broadinstitute.hellbender.tools.walkers.contamination
org.broadinstitute.hellbender.tools.walkers.coverage
org.broadinstitute.hellbender.tools.walkers.fasta
org.broadinstitute.hellbender.tools.walkers.featuremapping
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.groundtruth
org.broadinstitute.hellbender.tools.walkers.haplotypecaller
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.graphs
org.broadinstitute.hellbender.tools.walkers.haplotypecaller.ramps
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.sv
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.variantrecalling
org.broadinstitute.hellbender.tools.walkers.variantutils
org.broadinstitute.hellbender.tools.walkers.vqsr
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.data
org.broadinstitute.hellbender.tools.walkers.vqsr.scalable.modeling
org.broadinstitute.hellbender.transformers
org.broadinstitute.hellbender.utils
org.broadinstitute.hellbender.utils.activityprofile
org.broadinstitute.hellbender.utils.alignment
org.broadinstitute.hellbender.utils.baq
org.broadinstitute.hellbender.utils.bigquery
org.broadinstitute.hellbender.utils.bwa
org.broadinstitute.hellbender.utils.clipping
org.broadinstitute.hellbender.utils.clustering
org.broadinstitute.hellbender.utils.codecs
org.broadinstitute.hellbender.utils.codecs.copynumber
org.broadinstitute.hellbender.utils.codecs.gtf
org.broadinstitute.hellbender.utils.codecs.refseq
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.dragstr
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.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.R
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.spark
org.broadinstitute.hellbender.utils.svd
org.broadinstitute.hellbender.utils.text
org.broadinstitute.hellbender.utils.tsv	Utility classes to read and write tab separated value (tsv) files.
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.markduplicates
picard.sam.markduplicates.util
picard.sam.SamErrorMetric
picard.sam.util
picard.util
picard.util.help
picard.util.IntervalList
picard.vcf
picard.vcf.filter
picard.vcf.MendelianViolations
picard.vcf.processor
picard.vcf.processor.util