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``
Hi Brad,
Sounds good. Practically thinking, should I check if ``-U`` (and the following parameter) is in the command and then replace it?