GATK specifications

Information


Unique identifier OMICS_19453
Name Genome Analysis ToolKit
Software type Package/Module, Toolkit/Suite
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input format SAM, BAM, VCF, BED, DICT, FASTA, FAI, BAI
Output format SAM, BAM, VCF, BED
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License MIT License
Computer skills Advanced
Version 3.8.0
Stability Stable
High performance computing Yes
Registration required 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
  • 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
  • splitNcigar
  • ReCapSeg
  • Mutect2

Download


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Documentation


Maintainer


  • person_outline Geraldine Van der Auwera <>

Additional information


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

GATK articles

GATK institution(s)
Broad Institute, Cambridge, MA, USA; Massachusetts General Hospital, Boston, MA, USA

GATK review

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Arup Ghosh

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

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