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Hi,<br>
Unfortunately, it seems that the dbscSNV.pm module have some
bug. It detects the file, but do not extract the scores:<br>
- VEP v79 on genome version GRCh37 <br>
> echo "16 56548593 56548593 C/G" |
./variant_effect_predictor.pl --force_overwrite --database --port
3337 --dir_plugins ./cache/Plugins --plugin
dbscSNV,./datasets/vep/dbNSFP/dbscSNV.txt.gz<br>
<br>
- It added the 'ada_score' and 'rf_score' in the header but did not
extract any!<br>
<br>
- These coordinates are well in the file of dbscSNV.zip v1.0<br>
> zcat dbscSNV.txt.gz | grep --color -P '^16\t56548593\tC\tG'<br>
16 56548593 C G y y splicing
BBS2(NM_031885:exon3:c.118-1G>C) . . splicing
ENSG00000125124(ENST00000568104:exon3:c.118-1G>C;ENST00000245157:exon3:c.118-1G>C)
. . 0.999986675681007 0.932<br>
<br>
Could you help me with this issue please? Thanks.<br>
<br>
Regards,<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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