<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<p>Hi David,</p>
<p>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.<br>
</p>
<p>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.<br>
</p>
<p>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.</p>
<p>I will come back with a mail once the plugin is in.<br>
</p>
<p>Best regards,</p>
<p>Irina<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 21/02/2019 17:17, David Tamborero
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAMk_RaSkNpY6z4-KJeWbJwzv-QA1FhZE+3H9BovGVtt1DRtHGQ@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<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"
moz-do-not-send="true">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>
</div>
<blockquote type="cite">
<div dir="ltr">
<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>
<fieldset
class="gmail-m_-7639736395750451905mimeAttachmentHeader"></fieldset>
<pre class="gmail-m_-7639736395750451905moz-quote-pre">_______________________________________________
Dev mailing list <a class="gmail-m_-7639736395750451905moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org" target="_blank" moz-do-not-send="true">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="gmail-m_-7639736395750451905moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank" moz-do-not-send="true">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="gmail-m_-7639736395750451905moz-txt-link-freetext" href="http://www.ensembl.info/" target="_blank" moz-do-not-send="true">http://www.ensembl.info/</a>
</pre>
</blockquote>
<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" moz-do-not-send="true">ebi.ac.uk</a> | A3 - 135</pre>
</div>
</blockquote>
</div>
</blockquote>
<pre class="moz-signature" cols="72">-- </pre>
</body>
</html>