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    Hi Will,<br>
                Great news! <br>
    Thanks<br>
    Kirsley<br>
    <br>
    <br>
    <br>
    <div class="moz-cite-prefix">On 14/04/2015 17:18, Will McLaren
      wrote:<br>
    </div>
    <blockquote
cite="mid:CAMVEDX0EdroPpJj8woy5xR8FotSGvFbdH2WSMxgkaJqnQTvkqw@mail.gmail.com"
      type="cite">
      <div dir="ltr">Hi Kirsley,
        <div><br>
        </div>
        <div>The dbscSNV data works slightly differently than the dbNSFP
          data; I've added a separate plugin for this.</div>
        <div><br>
        </div>
        <div><a moz-do-not-send="true"
href="https://github.com/ensembl-variation/VEP_plugins/blob/master/dbscSNV.pm">https://github.com/ensembl-variation/VEP_plugins/blob/master/dbscSNV.pm</a><br>
        </div>
        <div><br>
        </div>
        <div>Note the different process for tabix-indexing the data
          file.</div>
        <div><br>
        </div>
        <div>Regards</div>
        <div><br>
        </div>
        <div>Will</div>
        <div><br>
        </div>
        <div><br>
        </div>
      </div>
      <div class="gmail_extra"><br>
        <div class="gmail_quote">On 8 April 2015 at 23:22, Kirsley
          Chennen <span dir="ltr"><<a moz-do-not-send="true"
              href="mailto:kchennen@unistra.fr" target="_blank">kchennen@unistra.fr</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="#000000"> Hi Will,<br>
                      Marvellous! Is it also possible to have an update
              of the <span
                style="font-size:10pt;background-color:transparent"></span><span
                style="background-color:transparent">dbNSFP.pm plugin,
                as </span><span
                style="font-size:10pt;background-color:transparent"></span><span
                style="background-color:transparent">dbNSFP[<a
                  moz-do-not-send="true"
                  href="https://sites.google.com/site/jpopgen/dbNSFP"
                  target="_blank">https://sites.google.com/site/jpopgen/dbNSFP</a>]
                now comes in two files; </span><span
                style="font-size:10pt;background-color:transparent"></span><span
                style="background-color:transparent">dbNSFP.XXX.zip for
                non-synonymous SNPs and dbscSNV.zip for splicing
                consensus regions? <br>
                Thanks again.<br>
                <br>
                Best regards,<br>
                Kirsley<br>
                <br>
                 </span>
              <div>
                <div class="h5"><br>
                  <br>
                  <div>On 08/04/2015 14:51, Will McLaren wrote:<br>
                  </div>
                  <blockquote type="cite">
                    <div dir="ltr">Hello,
                      <div><br>
                      </div>
                      <div>Looking at the CADD website, it seems the
                        data files for indels are separate from those
                        for SNVs.</div>
                      <div><br>
                      </div>
                      <div>I've updated the CADD plugin (<a
                          moz-do-not-send="true"
href="https://github.com/ensembl-variation/VEP_plugins/blob/master/CADD.pm"
                          target="_blank">https://github.com/ensembl-variation/VEP_plugins/blob/master/CADD.pm</a>)
                        to be able to run with more than one CADD data
                        file specified, e.g.:</div>
                      <div><br>
                      </div>
                      <div>perl <a moz-do-not-send="true"
                          href="http://variant_effect_predictor.pl"
                          target="_blank">variant_effect_predictor.pl</a>
                        [your_options] -plugin
                        CADD,whole_genome_SNVs.tsv.gz,InDels.tsv.gz<br>
                      </div>
                      <div><br>
                      </div>
                      <div>Hopefully this should work for you</div>
                      <div><br>
                      </div>
                      <div>Will McLaren</div>
                      <div>Ensembl Variation</div>
                    </div>
                    <div class="gmail_extra"><br>
                      <div class="gmail_quote">On 3 April 2015 at 10:32,
                        Kirsley CHENNEN <span dir="ltr"><<a
                            moz-do-not-send="true"
                            href="mailto:kchennen@unistra.fr"
                            target="_blank">kchennen@unistra.fr</a>></span>
                        wrote:<br>
                        <blockquote class="gmail_quote" style="margin:0
                          0 0 .8ex;border-left:1px #ccc
                          solid;padding-left:1ex">Hi,<br>
                              I would like to know how to use the CADD
                          plugin with VEP to annotate both SNP and
                          indels? In the plugin head description, it
                          seems to refer only to SNP. Is there a way to
                          annotate the indels too?<br>
                          <br>
                          <br>
                          Regards,<br>
                          Kirsley Chennen<br>
                        </blockquote>
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