<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>