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<p>Hello Will,</p>
<p>Good to know. We'll look forward in next VEP releases.</p>
<p>Thank you.</p>
<p>Regards,<br>
Guillermo.<br>
</p>
<br>
<div class="moz-cite-prefix">On 16/09/16 17:58, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX1k-F5iCXem0Y-veK0Yw9Gg1jPc-F9hHjYtMHB4Yo3ZBA@mail.gmail.com"
type="cite">
<div dir="ltr">Correct - this is an undesirable feature, in that
the allele check is useful for those sources where we do have
the alleles (the COSMIC limitations prevent us from storing the
alleles).
<div><br>
</div>
<div>We will fix this in a future VEP version.</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 16 September 2016 at 16:41,
Guillermo Marco Puche <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF">
<p>Hello Will,</p>
<p>Indeed I've both --check_existing and --check_alleles
enabled. If I disable --check_alleles COSMIC ids pop up.
So the only way of getting COSMIC is disabling allele
check?</p>
<p>Regards,<br>
Guillermo.<br>
</p>
<div>
<div class="h5"> <br>
<div>On 16/09/16 17:16, Will McLaren wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div>I don't see this issue - see attached
screenshot.</div>
<div><br>
</div>
<div>I've also tested with the local script
version and it works OK for me. Of course I'm
assuming you have --check_existing enabled if
you're running the script?</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 16 September 2016 at
12:37, Guillermo Marco Puche <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@<wbr>sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF">
<p>Dear devs,</p>
<p>I'm aware of the COSMIC licensing
changes. I'm trying to annotate a huge VCF
with latest vep (85). I'm not getting any
COSMIC annotation at all. The following
two VCF variants have COSMIC annotations
but I'm getting none with vep:<br>
</p>
<pre>chr1 69224 . A C
chr1 69230 . A C
</pre>
Has been COSMIC removed from Ensembl public
annotations even if VCF headers shows
COSMIC=77? I thought that the previous
releases would stay in Ensembl.<br>
<br>
Regards,<br>
Guillermo<br>
</div>
<br>
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