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

[David Tamborero]

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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