[ensembl-dev] local installation VEP - error in GMAF, EUR_MAF, EA_MAF

[Will McLaren]

Hello,

Apologies, the initial release 84 of VEP had a bug in that affects newer
(>=5.18) versions of Perl.

A fix [1] has already been applied to the ensembl-variation GitHub
repository, you can use INSTALL.pl to update VEP's API installation with
the fixed version.

Regards

Will McLaren
Ensembl Variation

[1] :
https://github.com/Ensembl/ensembl-variation/commit/e0b3b5129f67d51ac1beb2c0771291903154bcdf

On 25 April 2016 at 14:01, Honysová Barbora <Barbora.Honysova at gennet.cz>
wrote:

> Hello,
>
> after the installation of VEP84 (API and databases) with cache and plugins
> I have run variant effect predictor like usually. When I have checked my
> results returned, I have encountered the internal error when using a flag *--gmaf
> --maf_1kg --maf_exac --maf_esp* that no data have been received back into
> the final .txt file. If I try to run the same script, the version VEP83,
> using the databases and cache for version 83, I obtain the correct data.
> When running VEP84 and databases and cache 83, no results in these columns
> appear. If I use plugin dbNSFP, the corresponding values are received as
> well. But our internal database setup of data coming from NGS is not bulit
> to cope with different format using plugins.
>
> So, please, do you know what is going on or where to look for this error?
>
> Thanks, Bara
>
>
>
> Ing. Barbora Honysová
>
> Odborný VŠ pracovník v laboratorních metodách na oddělení molekulárně
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