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

[Irina Armean]

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 
> <mailto: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 <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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