code: def rnaseq_variant_calling(samples, run_parallel):
      
      samples = run_parallel("run_rnaseq_variant_calling", samples)
      variantcaller = dd.get_variantcaller(to_single_data(samples[0]))
      if variantcaller and ("gatk-haplotype" in variantcaller):
          out = []
          for d in joint.square_off(samples, run_parallel):
              out.extend([[to_single_data(xs)] for xs in multi.split_variants_by_sample(to_single_data(d))])
          samples = out
      if variantcaller:
          samples = run_parallel("run_rnaseq_ann_filter", samples)
      if variantcaller and ("gatk-haplotype" in variantcaller):
          out = []
          for data in (to_single_data(xs) for xs in samples):
              if "variants" not in data:
                  data["variants"] = []
              data["variants"].append({"variantcaller": "gatk-haplotype", "vcf": data["vrn_file_orig"],
                                       "population": {"vcf": data["vrn_file"]}})
              data["vrn_file"] = data.pop("vrn_file_orig")
              out.append([data])
          samples = out
      return samples
docs: run RNA-seq variant calling using GATK