Friday, December 9, 2011

GATK's available annotations

Perhaps because it changes too often, GATK's available annotations for VCF files does not seem to be online anywhere that I've seen. The GATK site says to run GATK with the "--list" parameter to list them. Doing that requires putting in valid input files and such. Basically, it's a pain.

So here's the list from GATK v1.3-21-gcb284ee


Available annotations for the VCF INFO field:
    ChromosomeCounts
    IndelType
    HardyWeinberg
    SpanningDeletions
    NBaseCount
    AlleleBalance
    MappingQualityZero
    LowMQ
    BaseCounts
    MVLikelihoodRatio
    InbreedingCoeff
    RMSMappingQuality
    TechnologyComposition
    HaplotypeScore
    SampleList
    QualByDepth
    FisherStrand
    SnpEff
    HomopolymerRun
    DepthOfCoverage
    MappingQualityZeroFraction
    GCContent
    MappingQualityRankSumTest
    ReadPosRankSumTest
    BaseQualityRankSumTest


Available annotations for the VCF FORMAT field:
    ReadDepthAndAllelicFractionBySample
    AlleleBalanceBySample
    DepthPerAlleleBySample
    MappingQualityZeroBySample


Available classes/groups of annotations:
    RodRequiringAnnotation
    StandardAnnotation
    WorkInProgressAnnotation
    ExperimentalAnnotation
    RankSumTest


No promises about how accurate this is for any other version.