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

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