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VariantAnnotator - when to use

KathKath Posts: 36Member


I am writing a pipeline to analyse exome sequencing data from families and would like some advice on using the VariantAnnotator walker. It seems I need to use VariantAnnotator prior to VariantRecalibrator as the latter relies on annotations generated by VariantAnnotator. Is this correct? Also, I would like to annotate my VCF using SNPeff and SNPsift. Can you suggest the best order in which to perform these steps. For example, my plan at the moment is to run steps in the following order: HaplotypeCaller, VariantAnnotator, VariantRecalibrator, ApplyRecalibration, PhaseByTransmission, ReadBackedPhasing, SNPeff, SNPsift.

Any help would be much appreciated,



  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,903Administrator, GATK Developer admin

    Hi Kath,

    The order you list here looks fine to me. Generally speaking many annotations can be added by the caller (either UnifiedGenotyper or HaplotypeCaller) by specifying them in the command line that you use for calling variants. However at this time some annotations are not available with HaplotypeCaller, and in such cases you do indeed need to run VariantAnnotator to add them.

    Geraldine Van der Auwera, PhD

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