RNA-seq variant calling preparations

As discussed previously, this will help push STAR aligned BAM files through the ``variant2`` pipeline for non-Gatk (and currently non-FreeBayes) variant callers, with the aim to eventually integrate parts of the ``variant2`` pipeline in ``RNA-seq``
Miika -- you're right. Sorry this code is not great as is and should really be checking for `-U` or `--unsafe` before adding the extra parameter like it does in line 225 further down. Apologies for the ugliness here. You should then be able to add `-U ALL` directly to `bcbio/variation/annotation.py` where you have the other change.