[ensembl-dev] can VEP output the distance of the variant to the exon junction?

Irina Armean iarmean at ebi.ac.uk
Fri Feb 22 16:48:14 GMT 2019

Hi David,

Thanks for the clarification and the positive feedback for the team. We 
do our best to make the desired functionality available in due time, 
sometimes it's easier/faster than other times.

We plan to add a VEP plugin within the next week, which will report the 
nearest exon junction boundary (exon id, bp distance, start or end, exon 
length) for variants in the protein coding region, this should answer 
your case and also provide some additional use cases.

For the case of frameshifts and premature stop codons, they are handled 
more efficiently in the main VEP code and is more complex to update 
quickly however we plan to cover this use case in the near future.

I will come back with a mail once the plugin is in.

Best regards,


On 21/02/2019 17:17, David Tamborero wrote:
> Hi Irina, thanks for your answer, it is always awesome how diligent 
> you are guys;
> my wishlist:
> - in my case, what i m interested in is in the distance (nucleotides) 
> from my variant 'within' the exon (ie protein coding-affecting 
> variant) to the next exon junction. But note that other users may be 
> interested in other distances, as those that you mention.
> - FYI, i m interested in that info for the variants that create 
> preamture stop codons, so I can estimate whether it will be likely 
> that the non-mediated decay is triggered (which depends on how far it 
> falls regarding the last junction of the transcript). Note that --for 
> the same reason-- I m also interested in, given a frameshift mutation, 
> where the new 'cryptic' stop codon will be placed. I currently 
> calculate it by actually using the VEP info that can be parsed from 
> the HGVSp column (e.g. p.Glu5ValfsTer5, meaning the stop codon in 5 
> codons after the first 'ectopic codon' created by the frameshift, if I 
> remember well).
> Again, I currently address both cases by my own ad hoc scripts, but I 
> thought that you already 'have' the info to easily output these 
> things, which I think it can be of interest for the community (and 
> surely more neat that my creepy coding!)
> hope it makes sense!
> br
> d
> El jue., 21 feb. 2019 a las 17:12, Irina Armean (<iarmean at ebi.ac.uk 
> <mailto:iarmean at ebi.ac.uk>>) escribió:
>     Dear David,
>     Thanks for the question. We currently don't have this
>     functionality however we can easily add the distance to the
>     closest exon.
>     To clarify, are you interested in getting the distance to the
>     nearest exon junction for the variants only when it affects a
>     protein coding transcript or also when they are
>     upstream/downstream of genes for example?
>     Best regards,
>     Irina
>     On 21/02/2019 11:09, David Tamborero wrote:
>>     Dear all,
>>     is any flag (which I cannot find) so the VEP output includes the
>>     distance of the (coding) variant to the closest exon junction?
>>     If not, somebody has a recommended fancy approach to do so? (My
>>     current approach is 'just' to match with my own script the VEP
>>     output for a given transcript with the exon coordinates data that
>>     can be retrieved in e.g. BioMart)
>>     many thanks in advance!
>>     d
>>     _______________________________________________
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>     -- 
>     Irina Armean PhD, Bioinformatican
>     Ensembl Variation, EMBL-EBI, Hinxton, UK
>     iarmean[at]ebi.ac.uk  <http://ebi.ac.uk>  | A3 - 135

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