GATK protocols

GATK specifications

Information


Unique identifier OMICS_19453
Name GATK
Alternative names Genome Analysis ToolKit, GenomeAnalysisTK
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 4.0
Stability Stable
High performance computing Yes
Registration required Yes
Maintained Yes

Subtools


  • AlleleBalance
  • AlleleBalanceBySample
  • AlleleCountBySample
  • AnalyzeCovariates
  • ApplyRecalibration
  • AS_FisherStrand
  • AS_InbreedingCoeff
  • AS_InsertSizeRankSum
  • AS_MappingQualityRankSumTest
  • AS_MQMateRankSumTest
  • AS_QualByDepth
  • AS_ReadPosRankSumTest
  • AS_RMSMappingQuality
  • AS_StrandOddsRatio
  • ASEReadCounter
  • BadCigarFilter
  • BadMateFilter
  • BaseCounts
  • BaseCountsBySample
  • BaseQualityRankSumTest
  • BaseQualitySumPerAlleleBySample
  • BaseRecalibrator
  • BeagleCodec
  • BedTableCodec
  • CalculateGenotypePosteriors
  • CallableLoci
  • CatVariants
  • ChromosomeCounts
  • ClippingRankSumTest
  • ClipReads
  • ClusteredReadPosition
  • CombineGVCFs
  • CombineVariants
  • CommandLineGATK
  • CompareCallableLoci
  • ContEst
  • CountBases
  • CountingFilteringIterator.CountingReadFilter
  • CountIntervals
  • CountLoci
  • CountMales
  • CountReadEvents
  • CountReads
  • CountRODs
  • CountRODsByRef
  • CountTerminusEvent
  • Coverage
  • DepthOfCoverage
  • DepthPerAlleleBySample
  • DepthPerSampleHC
  • DiagnoseTargets
  • DiffObjects
  • DuplicateReadFilter
  • ErrorRatePerCycle
  • ExcessHet
  • FailsVendorQualityCheckFilter
  • FastaAlternateReferenceMaker
  • FastaReferenceMaker
  • FastaStats
  • FindCoveredIntervals
  • FisherStrand
  • FlagStat
  • FractionInformativeReads
  • GatherBqsrReports
  • GATKPaperGenotyper
  • GCContent
  • GCContentByInterval
  • GenotypeConcordance
  • GenotypeGVCFs
  • GenotypeSummaries
  • HaplotypeCaller
  • HaplotypeResolver
  • HaplotypeScore
  • HardyWeinberg
  • HCMappingQualityFilter
  • HomopolymerRun
  • InbreedingCoeff
  • IndelRealigner
  • LeftAlignAndTrimVariants
  • LeftAlignIndels
  • LibraryReadFilter
  • LikelihoodRankSumTest
  • LowMQ
  • MalformedReadFilter
  • MappingQualityFilter
  • MappingQualityRankSumTest
  • MappingQualityUnavailableFilter
  • MappingQualityZero
  • MappingQualityZeroBySample
  • MappingQualityZeroFilter
  • MateSameStrandFilter
  • MaxInsertSizeFilter
  • MissingReadGroupFilter
  • MuTect2
  • Mutect2
  • MVLikelihoodRatio
  • NBaseCount
  • NoOriginalQualityScoresFilter
  • NotPrimaryAlignmentFilter
  • OverclippedReadFilter
  • OxoGReadCounts
  • PathSeq
  • PhaseByTransmission
  • Pileup
  • Platform454Filter
  • PlatformFilter
  • PlatformUnitFilter
  • PossibleDeNovo
  • PrintReads
  • PrintRODs
  • QCRef
  • QualByDepth
  • QualifyMissingIntervals
  • RandomlySplitVariants
  • RawHapMapCodec
  • ReadBackedPhasing
  • ReadClippingStats
  • ReadGroupBlackListFilter
  • ReadGroupProperties
  • ReadLengthDistribution
  • ReadLengthFilter
  • ReadNameFilter
  • ReadPosRankSumTest
  • ReadStrandFilter
  • RealignerTargetCreator
  • ReassignMappingQualityFilter
  • ReassignOneMappingQualityFilter
  • ReassignOriginalMQAfterIndelRealignmentFilter
  • ReCapSeg
  • RefSeqCodec
  • RegenotypeVariants
  • RMSMappingQuality
  • SAMPileupCodec
  • SampleFilter
  • SampleList
  • SAMReadCodec
  • SelectHeaders
  • SelectVariants
  • SimulateReadsForVariants
  • SingleReadGroupFilter
  • SpanningDeletions
  • splitNcigar
  • SplitNCigarReads
  • SplitSamFile
  • StrandAlleleCountsBySample
  • StrandBiasBySample
  • StrandOddsRatio
  • TableCodec
  • TandemRepeatAnnotator
  • TransmissionDisequilibriumTest
  • UnifiedGenotyper
  • UnmappedReadFilter
  • ValidateVariants
  • ValidationSiteSelector
  • VariantAnnotator
  • VariantEval
  • VariantFiltration
  • VariantRecalibrator
  • VariantsToAllelicPrimitives
  • VariantsToBinaryPed
  • VariantsToTable
  • VariantsToVCF
  • VariantType

Download


Versioning


Add your version

Documentation


Maintainers


Additional information


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

Publications for Genome Analysis ToolKit

GATK IN pipelines

 (954)
2018
PMCID: 5754367
PMID: 29302025
DOI: 10.1038/s41467-017-02306-5

[…] version 0.7.7) was used to map all reads to ucsc hg19. pcr duplicates were removed from alignments using picard version 1.96 (http://picard.sourceforge.net). indels were realigned using the genome analysis toolkit (gatk). snvs and short indels were called using gatk haplotype caller (version 3.4–46). all variants were annotated with annovar and in-house scripts, and most likely protein […]

2018
PMCID: 5754367
PMID: 29302025
DOI: 10.1038/s41467-017-02306-5

[…] used to map all reads to ucsc hg19. pcr duplicates were removed from alignments using picard version 1.96 (http://picard.sourceforge.net). indels were realigned using the genome analysis toolkit (gatk). snvs and short indels were called using gatk haplotype caller (version 3.4–46). all variants were annotated with annovar and in-house scripts, and most likely protein damage variants […]

2018
PMCID: 5754367
PMID: 29302025
DOI: 10.1038/s41467-017-02306-5

[…] were removed from alignments using picard version 1.96 (http://picard.sourceforge.net). indels were realigned using the genome analysis toolkit (gatk). snvs and short indels were called using gatk haplotype caller (version 3.4–46). all variants were annotated with annovar and in-house scripts, and most likely protein damage variants (nonsense, splice site, frameshift indel, and missense) […]

2018
PMCID: 5757203
PMID: 29379323
DOI: 10.2147/LCTT.S147841

[…] illumina (san diego, ca, usa) hiseq 2500® instrument., the raw fastq sequences obtained were aligned to human reference genome (grch37/hg19) using bwa program32,33 and processed using picard and gatk toolkits.34,35 the low frequency variants were identified using lofreq program. an in-house method has been developed to filter the low frequency variant to control false positive rate […]

2018
PMCID: 5760544
PMID: 29317692
DOI: 10.1038/s41598-017-18358-y

[…] tools were used to remove pcr-duplicated and multiple aligned reads. after filtering out low-quality reads with mapping quality < 13 and base quality < 13, snp calling was performed using gatk software. variants meeting the following three criteria were used for further analysis: (i) depth greater than 50x, (ii) quality value greater than 30, and (iii) allele frequency larger than 1% […]

GATK institution(s)
National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, IL, USA; Mayo Clinic, Department of Research Services, Rochester, MN, USA; Mayo Clinic, Department of IT Executive Administration, Rochester, MN, USA; Mayo Clinic, Department of Health Sciences Research, Rochester, MN, USA; Institute for Genomic Biology, University of Illinois at Urbana-Champaign, IL, USA; Department of Crop Sciences, University of Illinois at Urbana-Champaign, IL, USA; Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, IL, USA; Mayo Clinic, Department of Biochemistry and Molecular Biology, Rochester, MN, USA; Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, IL, USA
GATK funding source(s)
Supported by the Mayo Clinic Center for Individualized Medicine and the Todd and Karen Wanek Program for Hypoplastic Left Heart Syndrome.

GATK reviews

 (3)
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Sangram keshari sahu

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Desktop
A well maintained and active development tool in Genomics and they are expanding to other domains of NGS also (like transcriptomics). One of the best points about this tool is Adoption/Availability to different platforms. Starting from the command line to UI based Galaxy interphase and recently integration to all major cloud platforms from the development team itself.

Weisheng Wu

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Desktop
A very versatile package for most analyses involving genomic variants. Documentation is very informative and updated quickly.