[ensembl-dev] VEP cache for COSMIC variants

[D'Eletto, Michael]

Hi Ensembl dev team,

I had a question regarding the VEP caches and changes made to co-located COSMIC variants.  We've been using an older cache version of regulatory reasons in our lab, so I just noticed this update on new versions.  It seems that older versions of the cache (up until release 85) described the variant allele change in the cache, but starting in release 85, this variant allele change now says "COSMIC_MUTATION" instead.  Is there a reason for this change?  We found it useful for the VEP to report out only the COSMIC variant that matched that specific allele change (e.g. when using with --checking_existing) and not all COSMIC variants at a position.

    {
      "phenotype_or_disease": 1,
      "end": 21971208,
      "seq_region_name": 9,
      "somatic": 1,
      "allele_string": "COSMIC_MUTATION",
      "start": 21971208,
      "id": "COSM12537",
      "strand": 1
    }

Thanks,

Mike D'Eletto




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