code: def _segment_normalized_cnvkit(cnr_file, work_dir, paired):
      
      cnvkit_base = os.path.join(utils.safe_makedir(os.path.join(work_dir, "cnvkit")),
                                  dd.get_sample_name(paired.tumor_data))
      cnr_file = chromhacks.bed_to_standardonly(cnr_file, paired.tumor_data, headers="chromosome",
                                                  include_sex_chroms=True,
                                                  out_dir=os.path.dirname(cnvkit_base))
      cnr_file = _remove_overlaps(cnr_file, os.path.dirname(cnvkit_base), paired.tumor_data)
      seg_file = cnvkit.segment_from_cnr(cnr_file, paired.tumor_data, cnvkit_base)
      return cnr_file, seg_file
docs: Segmentation of normalized inputs using CNVkit.