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

[David Tamborero]

Thanks! Have a great weekend

El vie., 15 mar. 2019 18:31, Andrew Parton <aparton at ebi.ac.uk> escribió:

> 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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