[ensembl-dev] VEP cache for COSMIC variants

Sarah Hunt seh at ebi.ac.uk
Wed Mar 21 17:10:16 GMT 2018


Hi Mike,

COSMIC licensing has changed and the new terms longer permit us to 
redistribute the alleles observed. We can still provide locations and 
ids to allow you to look up information on the COSMIC site. There is 
full information here:

http://cancer.sanger.ac.uk/cosmic/license

Best wishes,

Sarah


On 21/03/2018 16:34, D'Eletto, Michael wrote:
>
> 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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