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

[David Tamborero]

thta s great, i m currently travelling but i will try it as soon as i back
to the lab (and feedback you guys as appropriate)

thanks again!
d

El vie., 1 mar. 2019 a las 16:27, Irina Armean (<iarmean at ebi.ac.uk>)
escribió:

> Hi David,
>
> The NearestExonJB.pm plugin is now available on github
> https://github.com/Ensembl/VEP_plugins. This plugin reports the nearest
> exon junction boundary (exon id, bp distance, start or end, exon length)
> within the affected transcript.
>
> I hope you find it useful.
>
> Best regards,
>
> Irina
> On 25/02/2019 08:40, David Tamborero wrote:
>
> That s fantastic, thanks!
>
> Have a great week
> D
>
> 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,
>>
>> Irina
>>
>>
>> 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>)
>> 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
>>>
>>> _______________________________________________
>>> 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/20190304/69c67b57/attachment.html>