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

Wed May 17 07:45:30 BST 2017

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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