<div dir="ltr">Hello,<div><br></div><div>To retrieve the HGVS notations, you call hgvs_coding or hgvs_protein on the TranscriptVariationAllele object passed to the run method in the plugin:</div><div><br></div><div><a href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1TranscriptVariationAllele.html">http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1TranscriptVariationAllele.html</a><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 29 January 2015 at 08:39, 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">
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Dear devs,<br>
<br>
If --hgvs option is enabled when running VEP is it possible to
retrieve HGVS for each transcript?<br>
I've been looking the documentation Will referenced me in previous
post,<br>
<br>
At first I thought I could retrieve it from "mapper" <br>
my $mapper =
$vf->transcript->{_variation_effect_feature_cache}->{mapper};<br>
<br>
however I've inspected the hash and I couldn't find it.<br>
<br>
Regards,<br>
Guillermo.<br>
</div>
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