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<div class="moz-cite-prefix">Thanks, Will, for taking care of this.
It would be great if it was also implemented for caches built out
of custom gene annotation with gtf2vep.pl.<br>
<br>
Cyriac, thanks for your suggestion, although in our case we are
greatly interested in finding the variant consequences in all the
annotated transcripts of the gene.<br>
<br>
Best,<br>
Jose<br>
<br>
<br>
<br>
On 09/06/16 15:26, Will McLaren wrote:<br>
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cite="mid:CAMVEDX1rK+Oe2vn9-VPgEm2_6_AVEA=G+hD+J8mUvNGx23bUhQ@mail.gmail.com"
type="cite">
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<div dir="ltr">Thanks Jose and Cyriac.
<div><br>
</div>
<div>This will be fixed in the next VEP release.</div>
<div><br>
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<div>Regards</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 8 June 2016 at 18:23, Cyriac Kandoth
<span dir="ltr"><<a moz-do-not-send="true"
href="mailto:kandoth@cbio.mskcc.org" target="_blank">kandoth@cbio.mskcc.org</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<p dir="ltr">Keeping variant consequence separate from the
quality of the transcript, neatly limits the complexity of
VEP. A solution for you, might be to pick and report the
consequence of the variant on the "canonical transcript".
Or maybe the transcript that is actually expressed in the
tissue you're studying. This is they motivation behind the
--pick and --pick-order options in VEP:</p>
<p dir="ltr"><a moz-do-not-send="true"
href="http://useast.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_pick"
target="_blank">http://useast.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_pick</a></p>
<span class="HOEnZb"><font color="#888888">
<p dir="ltr">~Cyriac</p>
</font></span>
<div class="HOEnZb">
<div class="h5">
<div class="gmail_quote">On Jun 8, 2016 6:37 AM, "Jose
M. Gonzalez" <<a moz-do-not-send="true"
href="mailto:jmg@sanger.ac.uk" target="_blank">jmg@sanger.ac.uk</a>>
wrote:<br type="attribution">
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Hi,<br>
<br>
We have noticed that VEP calls a "start_lost"
consequence on variants affecting the first codon of
transcripts with an incomplete CDS 5', i.e. those
tagged with a 'cds_start_NF' attribute. In most
cases this first codon is not even a canonical start
codon. Here is an example:<br>
<a moz-do-not-send="true"
href="http://www.ensembl.org/Homo_sapiens/Variation/Explore?db=core;g=ENSG00000116198;r=1:3829193-3829524;t=ENST00000461667;v=rs763522630;vdb=variation;vf=129057128"
rel="noreferrer" target="_blank">http://www.ensembl.org/Homo_sapiens/Variation/Explore?db=core;g=ENSG00000116198;r=1:3829193-3829524;t=ENST00000461667;v=rs763522630;vdb=variation;vf=129057128</a><br>
<br>
These are partial transcripts for which the true
start codon is not known, so we believe that a
"start_lost" consequence does not seem appropriate
in this case. Perhaps a consequence such as
"missense_variant" or "synonymous_variant" would be
more adequate for variants falling on these codons.<br>
<br>
Would it be possible for VEP to handle transcript
attributes indicating partial length in order to
call these types of consequences more accurately?<br>
<br>
Thanks,<br>
Jose<br>
<br>
-- <br>
Jose M. Gonzalez<br>
Senior Bioinformatician - GENCODE<br>
HAVANA Team<br>
Wellcome Trust Sanger Institute<br>
Hinxton, UK<br>
<br>
<br>
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