[ensembl-dev] can VEP produce co-located variants match taking account the protein change?

[Andrew Parton]

Hi David,

Thanks for the suggestion, we’ve had similar queries to this before. I’ll discuss it with the team on Monday and get back to you.

Kind Regards,
Andrew

> On 15 Mar 2019, at 14:01, David Tamborero <david.tamborero at gmail.com> wrote:
> 
> I received a weird @vep email, and now i m unsure of whether this was published (cannot see it in the archive), so I send it again. Apologies if this is not the case.
> 
> =
> 
> Hello there,
> 
> I m writing with further VEP whishes! The context is that I m matching the  variants given to VEP with the content of a given database(s) that report variant effects (e.g. biomarkers of drug response). I m currently passing these knowledgebases to VEP as a vcf (with the corresponding .tbi) with the --custom flag, which works lovely.
> 
> The thing is that I m also interested to have a match when the nucleotide change of the input variant is not the same than the one from the database *but* it leads to the same aminoacid change; something like:
> 
> database:  chr1:xxxxxA>C   (geneX p.V28E)
> 
> input:  chr1xxxxxxA>C   (geneX p.V28E)  produces a 'perfect match'
> input: chr1yyyyyyyG>T    (geneX p.V28E) produces an 'aminoacid match'
> 
> My plan is to keep using your --custom flag to retrieve the 'perfect' match and then to have my own script to retrieve the 'aminoacid match'. However, as you know, this is kind of a hassle (need to map the variants of the original databases with VEP to ensure that the protein statements are fully compatible, and I need to do it each time there is an update etc etc).
> 
> In other words, it would be more neat and easy if this 'aminoacid match' is provided by VEP given the --custom vcf file(s). By any chance, do you have some option (that I did not see) that magically does it, or any option that you can implement this in some incoming release?
> 
> (as for other requests, I think that this is a feature that would be useful for other users)
> 
> Thanks a lot in advance!
> br
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