code: def run_rnaseq_ann_filter(data):
      
      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]]
docs: Run RNA-seq annotation and filtering.