<div dir="ltr"><div dir="ltr"><div>Hi Irina, thanks for your answer, it is always awesome how diligent you are guys; <br></div><div><br></div><div>my wishlist:</div><div><br></div><div>- 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.</div><div><br></div><div>- 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).</div><div><br></div><div>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!)<br></div><div><br></div><div>hope it makes sense!</div><div>br</div><div>d<br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">El jue., 21 feb. 2019 a las 17:12, Irina Armean (<<a href="mailto:iarmean@ebi.ac.uk">iarmean@ebi.ac.uk</a>>) escribió:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<p>Dear David,</p>
<p>Thanks for the question. We currently don't have this
functionality however we can easily add the distance to the
closest exon.</p>
<p>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?</p>
<p>Best regards,</p>
<p>Irina</p>
<p><br>
</p>
<div class="gmail-m_-7639736395750451905moz-cite-prefix">On 21/02/2019 11:09, David Tamborero
wrote:<br>
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<blockquote type="cite">
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<div>Dear all, <br>
</div>
<div><br>
</div>
<div>is any flag (which I cannot find) so the VEP output
includes the distance of the (coding) variant to the closest
exon junction?</div>
<div><br>
</div>
<div>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)</div>
<div><br>
</div>
<div>many thanks in advance!</div>
<div>d<br>
</div>
</div>
<br>
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<pre class="gmail-m_-7639736395750451905moz-signature" cols="72">--
Irina Armean PhD, Bioinformatican
Ensembl Variation, EMBL-EBI, Hinxton, UK
iarmean[at]<a href="http://ebi.ac.uk" target="_blank">ebi.ac.uk</a> | A3 - 135</pre>
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