[ensembl-dev] VEP: Bug when using plugins from command line and config file

[Will McLaren]

Hi Guillermo,

Thanks for spotting this. The issue is fixed in ensembl-vep 88.9 (
https://github.com/Ensembl/ensembl-vep/commit/21069f158e4081ffc44d5389852a0e3da71fd7ff
).

Regards

Will McLaren
Ensembl Variation

On 17 May 2017 at 07:45, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:

> Dear devs,
>
> I've noticed a bug in latest VEP 88 version. If you activate more than one
> plugin, one in the config file and other directly in command line all the
> annotation fields produced by plugins are rendered empty. See the example
> below (my.conf would be the config file containing a line activating
> plugin):
>
> *vep -i input.vcf -o output.vcf -config my.conf -dir_plugins  dir_plugins -dir_cache .vep -plugin Test*
>
> I've managed to make this work "calling" all the plugins from command line.
>
> Regards,
> Guillermo
>
>
>
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