<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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            <br>
          </blockquote>
        </div>
        <br>
      </div>
      <br>
      <fieldset></fieldset>
      <br>
      <pre>______________________________<wbr>_________________
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</pre>
    </blockquote>
    <br>
    </div></div><div><br>
      <div align="center">
        <hr align="center" size="2" width="100%"></div>
    </div>
  </div>

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<br></blockquote></div><br></div>