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VariantAnnotator list option not working?

genecgenec Member
edited August 2012 in Ask the GATK team

The VariantAnnotator list option doesn't seem to be working. I just downloaded GATK Like 2.1.3, and I'm trying the command:

java -jar GenomeAnalysisTKLite.jar -T VariantAnnotator --list

But I just get the same help and error message (--variant argument is missing) as I would without the --list (or -ls) flag. Is this a bug or am I doing something wrong?

Thanks!

Best Answer

Answers

  • ebanksebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭
    Accepted Answer

    You need to use the full command-line even with --list. Just follow the instructions and you should be fine.

  • genecgenec Member

    Thanks, for the response. That then leads me to a comment/request:

    The documentation for UnifiedGenotyper says that I need to run VariantAnnotator -ls to get the list of possible annotations that I can have UnifiedGenotyper produce. But given the way that I have learned VariantAnnotator runs, I need to create a fully legitimate call to VariantAnnotator to simply get that list. My request is to allow UnifiedGenotyper and/or VariantAnnotator to produce the full list of potential annotations without having to actually do a VariantAnnotator full call.

    Thanks!

  • ebanksebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭

    Hi there,

    Thanks for the request, but unfortunately that's actually an extremely difficult thing to implement right now. Given that you'll need the reference and input VCF anyways, it's not unreasonable to ask that a user provide them for the --list option too.

  • rbagnallrbagnall Member

    I wanted to know the VariantAnnotator --list too.

    Following Eric's advice about using a full command, from GenomeAnalysisTK-2.1-13 the list was shown as:

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

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

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

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

  • grosscogrossco Member

    How do the classes/groups of annotations work? --annotation StandardAnnotation does not appear to be a valid argument. In the meantime I have simply listed all the standard annotations in the command line, but that seems much less convenient when there is an available class that encapsulates this list.

    -A BaseQualityRankSumTest -A DepthOfCoverage -A FisherStrand -A HaplotypeScore -A InbreedingCoeff -A MappingQualityRankSumTest -A MappingQualityZero -A QualByDepth -A RMSMappingQuality -A ReadPosRankSumTest -A SpanningDeletions -A TandemRepeatAnnotator
    
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi @grossco, what are you trying to do? FYI, the standard annotations are used by default by the callers, so you don't normally need to list them in your command line.

  • grosscogrossco Member

    I was tying to specify the list of annotations by class, since the --list option make not of the "Available classes/groups of annotations". It is of little consequence, since spelling out each and every annotation only has to be done once. I generally prefer to be very explicit about the options used so that I can make sense of what I have done when I come back to it in a few weeks. Having to go back to the documentation and see what the default parameters are or were just complicates things for me.

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