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

David Tamborero david.tamborero at gmail.com
Thu Feb 21 17:17:03 GMT 2019

Hi Irina, thanks for your answer, it is always awesome how diligent you are

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!

El jue., 21 feb. 2019 a las 17:12, Irina Armean (<iarmean at ebi.ac.uk>)

> 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 | A3 - 135
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