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

[Andrew Parton]

Hi David,

Hope you’re well. We’ve had a chat about this issue yesterday, unfortunately this is not something that we currently support, or could provide a quick fix for. However, we will be providing improvements to our protein annotations within the coming months, and we will keep this suggestion in mind if we feel this is something we could implement in the future.  

The easiest solution, as we see it, would be to run VEP on both files and compare the HGVSp outputs at the end.

Kind Regards,
Andrew

> On 15 Mar 2019, at 18:13, David Tamborero <david.tamborero at gmail.com> wrote:
> 
> Thanks! Have a great weekend 
> 
> El vie., 15 mar. 2019 18:31, Andrew Parton <aparton at ebi.ac.uk <mailto: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 <mailto: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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