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How do we view the specific annotations in each annotation group

Hi there, when using GATK4 you can provide an annotation group argument to tools such as halpotype caller. I am having difficulties finding out how to figure out what annotations belong to each group.

I've seen mentions of using --list with VariantAnnotator but that doesnt work with GATK4.

Any help?

Answers

  • SheilaSheila Broad InstituteMember, Broadie admin

    @pjongeneel
    Hi,

    Sorry about this, but there is no way to view the annotations belonging to each group. I am checking with the team if this is on their radar.

    -Sheila

  • MoneteMonete BrazilMember

    Hi,

    I don't know if @pjongeneel solved this problem. But I also have the same question every time that I had to choose some annotation.

    Since I couldn't find a complete answer, I put here my solution (sounds archaic, maybe there is something better than this, but it was the best I could do).

    To exhibit such list of available annotation, you need to use command below:

    java -jar .../GenomeAnalysisTK.jar -T VariantAnnotator -R .../ucsc.hg19.fasta -ls --variant .../your.vcf.gz
    

    Using such parameter "--list" (or -ls) on VariantAnnotator (GATK v3.8), it lists such things below (too long, so I put as spoiler):

    This is a list of available Variant Annotations for use with tools such as UnifiedGenotyper, HaplotypeCaller and VariantAnnotator. Please see the Technical Documentation for more details about these annotations:
    http://www.broadinstitute.org/gatk/tooldocs/

    Standard annotations in the list below are marked with a '*'.

    Available annotations for the VCF INFO field:
    AS_BaseQualityRankSumTest
    AS_FisherStrand
    AS_InbreedingCoeff
    AS_InsertSizeRankSum
    AS_MQMateRankSumTest
    AS_MappingQualityRankSumTest
    AS_QualByDepth
    AS_RMSMappingQuality
    AS_ReadPosRankSumTest
    AS_StrandOddsRatio
    AlleleBalance
    BaseCounts
    *BaseQualityRankSumTest
    *ChromosomeCounts
    ClippingRankSumTest
    ClusteredReadPosition
    *Coverage
    *ExcessHet
    *FisherStrand
    FractionInformativeReads
    GCContent
    GenotypeSummaries
    *HaplotypeScore
    HardyWeinberg
    HomopolymerRun
    *InbreedingCoeff
    LikelihoodRankSumTest
    LowMQ
    MVLikelihoodRatio
    *MappingQualityRankSumTest
    MappingQualityZero
    NBaseCount
    PossibleDeNovo
    *QualByDepth
    *RMSMappingQuality
    *ReadPosRankSumTest
    SampleList
    SnpEff
    SpanningDeletions
    *StrandOddsRatio
    TandemRepeatAnnotator
    TransmissionDisequilibriumTest
    VariantType

    Available annotations for the VCF FORMAT field:
    AlleleBalanceBySample
    AlleleCountBySample
    BaseCountsBySample
    BaseQualitySumPerAlleleBySample
    *DepthPerAlleleBySample
    DepthPerSampleHC
    MappingQualityZeroBySample
    OxoGReadCounts
    StrandAlleleCountsBySample
    StrandBiasBySample

    Available classes/groups of annotations:
    AS_RMSAnnotation
    AS_RankSumTest
    AS_StandardAnnotation
    AS_StrandBiasTest
    ActiveRegionBasedAnnotation
    BetaTestingAnnotation
    ExperimentalAnnotation
    RMSAnnotation
    RankSumTest
    ReducibleAnnotation
    RodRequiringAnnotation
    StandardAnnotation
    StandardHCAnnotation
    StandardSomaticAnnotation
    StandardUGAnnotation
    StrandBiasTest
    WorkInProgressAnnotation

    But, I couldn't find anywhere a summary of which annotations each group of annotations (or classes) deals. So I did this search manually (one by one) in this link.

    I put the result here (attached below).

    In this file, there is the description of each annotation and the group of annotations related to. The "Type" in some annotations (i. e., ActiveRegionBasedAnnotation, or StandardAnnotation), is the group of annotations (parameter "--group") you can use in variantannotator (or other). The "Type NA", you need to use this annotation like "--annotation NBaseCount".

    Like I said, maybe there is some better solution (indeed, much better). Also, I don't know if it is complete. But it was the best I could do with the knowledge and tools which I had.

    Hope this helps!

  • pjongeneelpjongeneel Member

    thanks Monete! Appreciate the reply! No I never solved the problem, but this solution works, so thank you. Hopefully the code or a documentation page gets updated soon that makes this much easier in the future.

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