In gatk4, my understanding is that SnpEff has been superceded (now years ago). My question relates to cohort calling of hundreds of WES samples using the workflow. GenotypeGVCF has been run on the GenomicsDB to yield a joint vcf.
Are all required annotations for VariantRecalibrator now present following GenotypeGVCF? I know the Broad does not support SnpEff any longer but is there any value in adding external annotations prior to the VariantRecalibrator step using VariantAnnotator or Funcotator, or is it best to leave additional VCF annotation till later? I note Funcotator is specifically mentioned only for per-sample calling in the Best Practice Guidelines. Any experience with this would be appreciated.
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