run RNA-seq variant calling, variation file is stored in `vrn_file`
    in the datadict

def run_rnaseq_variant_calling(data):
    """
    run RNA-seq variant calling, variation file is stored in `vrn_file`
    in the datadict
    """
    variantcaller = dd.get_variantcaller(data)
    if isinstance(variantcaller, list) and len(variantcaller) > 1:
        logger.error("Only one variantcaller can be run for RNA-seq at "
                     "this time. Post an issue here "
                     "(https://github.com/bcbio/bcbio-nextgen/issues) "
                     "if this is something you need to do.")
        sys.exit(1)

    if variantcaller:
        if "gatk-haplotype" in variantcaller:
            data = variation.rnaseq_gatk_variant_calling(data)
        if vardict.get_vardict_command(data):
            data = variation.rnaseq_vardict_variant_calling(data)
        vrn_file = dd.get_vrn_file(data)
    return [[data]]