def run_rnaseq_ann_filter(data):
    """Run RNA-seq annotation and filtering.
    """
    data = to_single_data(data)
    if dd.get_vrn_file(data):
        eff_file = effects.add_to_vcf(dd.get_vrn_file(data), data)[0]
        if eff_file:
            data = dd.set_vrn_file(data, eff_file)
        ann_file = population.run_vcfanno(dd.get_vrn_file(data), data)
        if ann_file:
            data = dd.set_vrn_file(data, ann_file)
    variantcaller = dd.get_variantcaller(data)
    if variantcaller and ("gatk-haplotype" in variantcaller):
        filter_file = variation.gatk_filter_rnaseq(dd.get_vrn_file(data), data)
        data = dd.set_vrn_file(data, filter_file)
    # remove variants close to splice junctions
    vrn_file = dd.get_vrn_file(data)
    vrn_file = variation.filter_junction_variants(vrn_file, data)
    data = dd.set_vrn_file(data, vrn_file)
    return [[data]]
Run RNA-seq annotation and filtering.