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

Honysová Barbora Barbora.Honysova at gennet.cz
Mon Apr 25 14:49:07 BST 2016


Great, thank you, it works now.
Bara

From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Will McLaren
Sent: Monday, April 25, 2016 3:28 PM
To: Ensembl developers list
Subject: Re: [ensembl-dev] local installation VEP - error in GMAF, EUR_MAF, EA_MAF

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<mailto: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

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Ing. Barbora Honysová

Odborný VŠ pracovník v laboratorních metodách na oddělení molekulárně genetické laboratoře - konzultant

GENNET, s.r.o.



Kostelní 9, 170 00 Praha 7
Tel: +420 222 313 000

www.gennet.cz<http://www.gennet.cz>



[cid:image90cf74.GIF at 84d95641.4ebb2db7]



Where excellence meets hope

Tento e-mail včetně jeho případných příloh je určen výlučně pro adresáta uvedeného v záhlaví e-mailové zprávy. Disclaimer je k nahlédnutí zde<http://www.gennet.cz/disclaimer/> GENNET s.r.o. je českou společností registrovanou pod IČ 27080234 se sídlem Kostelní 9, Praha 7.

This email communication including any attachments is intended solely for the user of the email address to which it was addressed. Please click here<http://www.gennet.cz/disclaimer/><http://www.gennet.cz/disclaimer.html> to see our disclaimer. GENNET is a Czech limited liability company (VAT ID CZ699004108). Its registered office is at Kostelni 9, Prague, Czech Republic.

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