<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 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 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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