code: def _run_paired(paired):
      
      from bcbio.structural import titancna
      work_dir = _sv_workdir(paired.tumor_data)
      seg_files = model_segments(tz.get_in(["depth", "bins", "normalized"], paired.tumor_data),
                                 work_dir, paired)
      call_file = call_copy_numbers(seg_files["seg"], work_dir, paired.tumor_data)
      out = []
      if paired.normal_data:
          out.append(paired.normal_data)
      if "sv" not in paired.tumor_data:
          paired.tumor_data["sv"] = []
      paired.tumor_data["sv"].append({"variantcaller": "gatk-cnv",
                                      "call_file": call_file,
                                      "vrn_file": titancna.to_vcf(call_file, "GATK4-CNV", _get_seg_header,
                                                                  _seg_to_vcf, paired.tumor_data),
                                      "seg": seg_files["seg"],
                                      "plot": plot_model_segments(seg_files, work_dir, paired.tumor_data)})
      out.append(paired.tumor_data)
      return out
docs: Run somatic variant calling pipeline.