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Genome Analysis ToolKit GATK

Focuses on variant discovery and genotyping. GATK provides a toolkit, developed at the Broad Institute, composed of several tools and ables to support projects of any size. The application compiles an assortment of command line allowing one to analyze of high-throughput sequencing (HTS) data in various formats such as SAM, BAM, CRAM or VCF. The website includes multiple documentation for guiding users.

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1 user review

1 user review

Arup Ghosh's avatar image Arup Ghosh's country flag

Arup Ghosh

One of the best command-line based tools for variant calling from the aligned files with a variety of options for analysis.

GATK forum

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GATK classification

GATK specifications

Software type:
Package/Module, Toolkit/Suite
Restrictions to use:
Academic or non-commercial use
Programming languages:
Java
Computer skills:
Advanced
Stability:
Stable
Registration required:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
MIT License
Version:
3.8.0
High performance computing:
Yes
Maintained:
Yes

Subtools

  • CommandLineGATK
  • ASEReadCounter
  • AnalyzeCovariates
  • CallableLoci
  • CompareCallableLoci
  • ContEst
  • CountBases
  • CountIntervals
  • CountLoci
  • CountMales
  • CountRODs
  • CountRODsByRef
  • CountReadEvents
  • CountReads
  • CountTerminusEvent
  • DepthOfCoverage
  • DiagnoseTargets
  • DiffObjects
  • ErrorRatePerCycle
  • FastaStats
  • FlagStat
  • FindCoveredIntervals
  • GCContentByInterval
  • GatherBqsrReports
  • Pileup
  • PrintRODs
  • QualifyMissingIntervals
  • ReadClippingStats
  • ReadGroupProperties
  • ReadLengthDistribution
  • SimulateReadsForVariants
  • BaseRecalibrator
  • ClipReads
  • IndelRealigner
  • LeftAlignIndels
  • PrintReads
  • RealignerTargetCreator
  • SplitNCigarReads
  • SplitSamFile
  • ApplyRecalibration
  • CalculateGenotypePosteriors
  • GATKPaperGenotyper
  • GenotypeGVCFs
  • HaplotypeCaller
  • MuTect2
  • RegenotypeVariants
  • UnifiedGenotyper
  • VariantRecalibrator
  • GenotypeConcordance
  • ValidateVariants
  • VariantEval
  • VariantFiltration
  • CatVariants
  • CombineGVCFs
  • CombineVariants
  • HaplotypeResolver
  • LeftAlignAndTrimVariants
  • PhaseByTransmission
  • RandomlySplitVariants
  • ReadBackedPhasing
  • SelectHeaders
  • SelectVariants
  • ValidationSiteSelector
  • VariantAnnotator
  • VariantsToAllelicPrimitives
  • VariantsToBinaryPed
  • VariantsToTable
  • VariantsToVCF
  • AS_FisherStrand
  • AS_InbreedingCoeff
  • AS_InsertSizeRankSum
  • AS_MQMateRankSumTest
  • AS_MappingQualityRankSumTest
  • AS_QualByDepth
  • AS_RMSMappingQuality
  • AS_ReadPosRankSumTest
  • AS_StrandOddsRatio
  • AlleleBalance
  • AlleleBalanceBySample
  • AlleleCountBySample
  • BaseCounts
  • BaseCountsBySample
  • BaseQualityRankSumTest
  • BaseQualitySumPerAlleleBySample
  • ChromosomeCounts
  • ClippingRankSumTest
  • ClusteredReadPosition
  • Coverage
  • DepthPerAlleleBySample
  • DepthPerSampleHC
  • ExcessHet
  • FisherStrand
  • FractionInformativeReads
  • GCContent
  • GenotypeSummaries
  • HaplotypeScore
  • HardyWeinberg
  • HomopolymerRun
  • InbreedingCoeff
  • LikelihoodRankSumTest
  • LowMQ
  • MVLikelihoodRatio
  • MappingQualityRankSumTest
  • MappingQualityZero
  • MappingQualityZeroBySample
  • NBaseCount
  • OxoGReadCounts
  • PossibleDeNovo
  • QualByDepth
  • RMSMappingQuality
  • ReadPosRankSumTest
  • SampleList
  • SnpEff
  • SpanningDeletions
  • StrandAlleleCountsBySample
  • StrandBiasBySample
  • StrandOddsRatio
  • TandemRepeatAnnotator
  • TransmissionDisequilibriumTest
  • VariantType
  • BadCigarFilter
  • BadMateFilter
  • CountingFilteringIterator.CountingReadFilter
  • DuplicateReadFilter
  • FailsVendorQualityCheckFilter
  • HCMappingQualityFilter
  • LibraryReadFilter
  • MalformedReadFilter
  • MappingQualityFilter
  • MappingQualityUnavailableFilter
  • MappingQualityZeroFilter
  • MateSameStrandFilter
  • MaxInsertSizeFilter
  • MissingReadGroupFilter
  • NoOriginalQualityScoresFilter
  • NotPrimaryAlignmentFilter
  • OverclippedReadFilter
  • Platform454Filter
  • PlatformFilter
  • PlatformUnitFilter
  • ReadGroupBlackListFilter
  • ReadLengthFilter
  • ReadNameFilter
  • ReadStrandFilter
  • ReassignMappingQualityFilter
  • ReassignOneMappingQualityFilter
  • ReassignOriginalMQAfterIndelRealignmentFilter
  • SampleFilter
  • SingleReadGroupFilter
  • UnmappedReadFilter
  • BeagleCodec
  • BedTableCodec
  • RawHapMapCodec
  • RefSeqCodec
  • SAMPileupCodec
  • SAMReadCodec
  • TableCodec
  • FastaAlternateReferenceMaker
  • FastaReferenceMaker
  • QCRef

GATK distribution

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GATK support

Documentation

Maintainer

  • Geraldine Van der Auwera <>

Additional information

https://software.broadinstitute.org/gatk/documentation/quickstart.php

Credits

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Publications

Institution(s)

Broad Institute, Cambridge, MA, USA; Massachusetts General Hospital, Boston, MA, USA

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.