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Hi again Will,<br>
I have a l'll question concerning dbNSFP data. With the
latest release (<span style="background-color:transparent">dbNSFP3.0b2a,
dbscSNV)</span><big><big><span
style="font-size:10pt;background-color:transparent"></span></big></big>,
by default the tabix indexing is on the hg38 coordinates, but if I
want to use hg19 coordinates, will the following tabix indexing
work?<br>
<br>
tabix -s 1 -b 9 -e 9 dbNSFP.gz<br>
<br>
Columns of dbNSFP_variant:<br>
chr: chromosome number<br>
pos(1-based): physical position on the chromosome as to hg38
(1-based coordinate).<br>
For mitochondrial SNV, this position refers to the rCRS
(GenBank: NC_012920). <br>
ref: reference nucleotide allele (as on the + strand)<br>
alt: alternative nucleotide allele (as on the + strand)<br>
aaref: reference amino acid<br>
"." if the variant is a splicing site SNP (2bp on each end
of an intron)<br>
aaalt: alternative amino acid<br>
"." if the variant is a splicing site SNP (2bp on each end
of an intron)<br>
rs_dbSNP142: rs number from dbSNP 142<br>
hg19_chr: chromosome as to hg19, "." means missing<br>
hg19_pos(1-based): physical position on the chromosome as to
hg19 (1-based coordinate).<br>
For mitochondrial SNV, this position refers to a YRI
sequence (GenBank: AF347015)<br>
.<br>
.<br>
.<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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