[ensembl-dev] HGVS formatted genomic change

[Will McLaren]

Hi Mollie,

The functionality isn't there currently, but is super-easy to implement in
a plugin. Here's a quickie couple of lines to get the job done:

> echo 'package HGVSg; use Bio::EnsEMBL::Variation::Utils::BaseVepPlugin;
use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin); sub run { my
$vf = $_[1]->variation_feature; return { HGVSg => join(",", values
%{$vf->hgvs_genomic($vf->slice)}) }} 1;' > HGVSg.pm
> perl variant_effect_predictor.pl -cache -i example_GRCh38.vcf -plugin
HGVSg

Regards

Will

On 28 July 2015 at 14:54, Ullman-Cullere, Mollie <
MULLMANCULLERE at partners.org> wrote:

>  Is there a way to get HGVS formatted genomic change from standalone
> implementation of VEP?
>
>
>
> If not, is this going  to be added in the future?
>
>
>
> Thanks,
>
> Mollie
>
>
>
>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20150728/f91654d8/attachment.html>