Ensembl/ensembl-variation — pull request #2 by tweep (2014-03-26 19:55:53+00:00)
Title: E74 limit transcript effect gene source

Hi Will,

I've added an option to the pipeline which calculates the consequences of variations - this option allows to limit the types of genes which are used for the analysis. Reason for this is that we have different gene sets with different logic names, and we only want to calculate the consequences for some gene sets but not for all.

The default behaviour is to fetch all genes ( that is, if no gene biotypes have been configured). The option is named "limit_biotype" in the VariationConsequence_conf.pm file.

Would be great if that could be merged into the trunk. I've used it in Branch 74.