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 -- instead of changing this globally for every GATK call, could we add `-U ALL` to the parameters when we need it? If I understood right, that is only with GATK post-annotation of VCFs, or is there another spot?