[BioC] ensemblVEP, variant_effect_predictor versions and release schedule

[Thomas Sandmann [guest]]

Dear Valerie,

Currently, the documentation for your ensemblVEP package (BioC 2.13) indicates that variant_effect_predictor.pl from ensemble release 73 is required. 

I was wondering if had any plans on supporting different versions of ensembl's variant_effect_predictor.pl script with your ensemblVEP package.

As far as I know, ensembl is on a pretty rapid release schedule, most likely faster than the 6 month schedule of BioC. This is often also too fast for many users (and our company), who update less frequently than ensembl itself, relying on previous ensembl and variant_effect_predictor versions. For example, we are currently still using the database schemas and tools of ensembl 67.

The variant_effect_predictor.pl script also evolves with the ensembl releases. For example, new command line parameters have been added in recent versions ( e.g. --database, --dir_cache, --dir_plugins) and others have been modified (e.g. the handling of plugins).

Would you mind sharing your thoughts on how you are planning to support past and / or future versions of variant_effect_predictor.pl ? For example, are you planning to explicitly support a single version with every ensemblVEP release ? Or would it be possible to include a 'version' parameter in ensemblVEP to switch between parameters supported by different versions of the perl script ?

Thanks a lot for any insights,
Thomas

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