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

Irina Armean iarmean at ebi.ac.uk
Thu Feb 21 16:12:32 GMT 2019

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,


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
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

Irina Armean PhD, Bioinformatican
Ensembl Variation, EMBL-EBI, Hinxton, UK
iarmean[at]ebi.ac.uk | A3 - 135

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20190221/e53f1651/attachment.html>

More information about the Dev mailing list