<div dir="ltr">Hello,<div><br></div><div style>Some variants are parsed by the VEP as structural variants, and these are treated subtly differently as typically they are much larger than regular sequence variants.</div><div style>
<br></div><div style>To enable your plugin to process both types, you should use:</div><div style><br></div><div style>return ['BaseVariationFeature'];</div><div style><br></div><div style>or for just structural variants</div>
<div style><br></div><div style>return ['StructuralVariationFeature'];</div><div style><br></div><div style>Regards</div><div style><br></div><div style>Will</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On 9 May 2013 10:33, 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 bgcolor="#FFFFFF" text="#000066">
    <div>Hello,<br>
      <br>
      Ok this seems to clarify all.<br>
      <br>
      What about plugins with also variant_feature_types sub-routine?<br>
      <br>
      sub variant_feature_types {<br>
          return ['VariationFeature'];<br>
      }<br>
      <br>
      Thank you.<br>
      <br>
      Best regards,<br>
      Guillermo.<div><div class="h5"><br>
      <br>
      On 05/09/2013 10:19 AM, Will McLaren wrote:<br>
    </div></div></div><div><div class="h5">
    <blockquote type="cite">
      <div dir="ltr">Hi Guillermo,
        <div><br>
        </div>
        <div>The feature_types sub determines when the plugin
          is run depending on what feature type the
          TranscriptVariationAllele object overlaps.</div>
        <div><br>
        </div>
        <div>
          To enable your plugin to run on every variant, regardless of
          what it overlaps, you should have the sub return:</div>
        <div><br>
        </div>
        <div>return ['Feature','Intergenic'];</div>
        <div><br>
        </div>
        <div>Remove 'Intergenic' if you don't want the plugin
          to run on variants that don't overlap a transcript or
          regulatory feature.</div>
        <div><br>
        </div>
        <div>'Feature' is a catch-all type that includes
          transcripts and regulatory feature types.</div>
        <div><br>
        </div>
        <div>Hope this helps</div>
        <div><br>
        </div>
        <div>Will</div>
      </div>
      <div class="gmail_extra"><br>
        <br>
        <div class="gmail_quote">On 9 May 2013 08:11, 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 bgcolor="#FFFFFF" text="#000066"> Hello,<br>
              <br>
              While I'm using VEP flag "--regulatory" flag I notice a
              weird output in my vep file.<br>
              Some lines present all empty columns except: Consequence,
              Feature and Feature_type.<br>
              <br>
              While I'm using VEP plugin Conservation (available in VEP
              github repository) some lines present all empty columns
              except: Consequence, Feature, Feature_type and
              Conservation.<br>
              <br>
              I would like that the rest of my columns (obtained from
              VCF through plugin) are also show. I think this has
              something to do with the following lines in my plugin:<br>
              <br>
              <pre>sub feature_types {</pre>
              <pre>    return ['Transcript'];</pre>
              <pre>}

</pre>
              I'm am wrong?<br>
              <br>
              Thank you !<br>
              <br>
              Best regards,<br>
              Guillermo.<br>
            </div>
            <br>
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            <br>
          </blockquote>
        </div>
        <br>
      </div>
      <br>
      <fieldset></fieldset>
      <br>
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</pre>
    </blockquote>
  </div></div></div>

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