[ensembl-dev] can VEP output the distance of the variant to the exon junction?
david.tamborero at gmail.com
Mon Feb 25 08:40:20 GMT 2019
That s fantastic, thanks!
Have a great week
El vie., 22 feb. 2019 17:48, Irina Armean <iarmean at ebi.ac.uk> escribió:
> 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!
> 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,
>> 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.
>> many thanks in advance!
>> Dev mailing list Dev at ensembl.org
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>> Ensembl Blog: http://www.ensembl.info/
>> Irina Armean PhD, Bioinformatican
>> Ensembl Variation, EMBL-EBI, Hinxton, UK
>> iarmean[at]ebi.ac.uk | A3 - 135
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