[ensembl-dev] VEP retrieve HGVS

[Will McLaren]

Hello,

To retrieve the HGVS notations, you call hgvs_coding or hgvs_protein on the
TranscriptVariationAllele object passed to the run method in the plugin:

http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1TranscriptVariationAllele.html

Regards

Will McLaren
Ensembl Variation

On 29 January 2015 at 08:39, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:

>  Dear devs,
>
> If --hgvs option is enabled when running VEP is it possible to retrieve
> HGVS for each transcript?
> I've been looking the documentation Will referenced me in previous post,
>
> At first I thought I could retrieve it from "mapper"
> my $mapper = $vf->transcript->{_variation_effect_feature_cache}->{mapper};
>
> however I've inspected the hash and I couldn't find it.
>
> Regards,
> Guillermo.
>
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