<div dir="ltr">If you enable the --check_existing flag when you run the VEP, you'll be able to see any known co-located variants attached to the VariationFeature object in your plugin:<div><br></div><div>sub run {</div> my $self = shift;<div> my $tva = shift;</div><div> my $vf = $tva->variation_feature;</div><div><br></div><div> foreach my $known_var(@{$vf->{existing} || []}) {</div><div> # do stuff</div><div> }</div><div>}</div><div><br></div><div>The $known_var is not an API object but a simple hashref with a number of fields; you're probably interested in $known_var->{clin_sig}</div><div><br></div><div>However, as I mentioned, this is the only data that is stored in the cache. To access the rating and the specific disease association, you'll need to make calls to the database by getting an adaptor, something like:</div><div><br></div><div><div>sub run {</div><div> my $self = shift;</div><div> my $tva = shift;</div><div> my $vf = $tva->variation_feature;</div><div> my $pfa = $self->{config}->{reg}->get_adaptor('human','variation','phenotypefeature');</div><div><br></div><div> foreach my $known_var(@{$vf->{existing} || []}) {</div><div> foreach my $pf(@{$pfa->fetch_all_by_object_id($known_var->{variation_name})}) {</div><div> # do stuff</div><div> }</div><div> }</div><div>}</div></div><div><br></div><div>Be aware that this will access the database, so unless you have a local copy please don't run this sort of code on genome-wide VCFs using our public DB server.</div><div><br></div><div>Regards</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 2 March 2015 at 14:47, Guillermo Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF">
Hi Will,<br>
<br>
Indeed I'm looking to retrieve this information from VEP plugin.<br>
<br>
Regards,<br>
Guillermo.<div><div class="h5"><br>
<br>
<div>On 02/03/15 15:25, Will McLaren wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div>The detailed ClinVar information is stored against
PhenotypeFeature objects (each SNP/disease pairing gets its
own entry in ClinVar, e.g. <a href="http://www.ncbi.nlm.nih.gov/clinvar/RCV000019691.2" target="_blank">http://www.ncbi.nlm.nih.gov/clinvar/RCV000019691.2</a>, <a href="http://www.ncbi.nlm.nih.gov/clinvar/RCV000019692.2/" target="_blank">http://www.ncbi.nlm.nih.gov/clinvar/RCV000019692.2/</a>, <a href="http://www.ncbi.nlm.nih.gov/clinvar/RCV000019693.2/" target="_blank">http://www.ncbi.nlm.nih.gov/clinvar/RCV000019693.2/</a>
for rs699).</div>
<div><br>
</div>
<div>The rating (and indeed the clinical significance) is stored
as an attribute on the PhenotypeFeature object; you can
retrieve this with the get_all_attributes() method.</div>
<div><br>
</div>
<div>See <a href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1PhenotypeFeature.html" target="_blank">http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1PhenotypeFeature.html</a>
and <a href="http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype" target="_blank">http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#phenotype</a>
for more info.</div>
<div><br>
</div>
<div><span style="font-size:12.8000001907349px">Bio::EnsEMBL::Variation::</span><span style="font-size:12.8000001907349px">Utils::VEP::get_clin_sig()
is an internal method that you should not use.</span></div>
<div><span style="font-size:12.8000001907349px"><br>
</span></div>
<div><span style="font-size:12.8000001907349px">The VEP cache
contains the list of clinical significance states for each
variant, but neither the disease association or the rating.
If you want help getting access to this data via a plugin,
let me know as it's a little more involved than the API
methods above (though it is faster as no database access is
required).</span><br>
</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 2 March 2015 at 14:06, Guillermo
Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF"> Dear devs,<br>
<br>
I'm looking forward to retrieve ClinVar information and
add it to VEP annotation. From my understanding I should
be able to retrieve "Clinical significance" and "ClinVar
Rating".<br>
<br>
I've been looking the Varation API, and I'm confused. I
guess for significance I should use
Bio::EnsEMBL::Variation::Utils::VEP::get_clin_sig() or
Bio::EnsEMBL::Variation::VariationFeature::get_all_clinical_significance_states().<br>
<br>
What about ClinVar rating? Is it possible to retrieve it
from API?<br>
<br>
Thanks!<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
<br>
</div>
<br>
_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
</div>
<br>
<fieldset></fieldset>
<br>
<pre>_______________________________________________
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
</div></div><div>-- <br>
<div align="center">
<hr size="2" width="100%" align="center"></div>
<table cellpadding="0" align="center" border="0">
<tbody>
<tr>
<td>
<p><span style="font-size:12px"><span style="font-family:arial,helvetica,sans-serif"><span style="color:#000066"><strong>Guillermo Marco
Puche</strong><br>
<br>
Bioinformatician, Computer Science Engineer<br>
Sistemas Genómicos S.L.<br>
Phone: <a href="tel:%2B34%20902%20364%20669" value="+34902364669" target="_blank">+34 902 364 669</a> (Ext.777)<br>
Fax: <a href="tel:%2B34%20902%20364%20670" value="+34902364670" target="_blank">+34 902 364 670</a></span><br>
<a href="http://www.sistemasgenomicos.com" target="_blank"><span style="color:#000066">www.sistemasgenomicos.com</span></a></span></span></p>
</td>
<td>
<p><a href="https://www.sistemasgenomicos.com/web_sg/web/areas-bioinformatica.php" target="_blank"><img alt="" src="cid:part11.06080203.01040703@sistemasgenomicos.com">
</a></p>
</td>
</tr>
</tbody>
</table>
<div align="center">
<hr size="2" width="100%" align="center"></div>
</div>
</div>
<br>_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div><br></div>