code: def filter_multimappers(align_file, data):
      
      config = dd.get_config(data)
      type_flag = "" if bam.is_bam(align_file) else "S"
      base, ext = os.path.splitext(align_file)
      out_file = base + ".unique" + ext
      bed_file = dd.get_variant_regions(data) or dd.get_sample_callable(data)
      bed_cmd = '-L {0}'.format(bed_file) if bed_file else " "
      if utils.file_exists(out_file):
          return out_file
      base_filter = '-F "not unmapped {paired_filter} and not duplicate and [XA] == null and [SA] == null and not supplementary " '
      if bam.is_paired(align_file):
          paired_filter = "and paired and proper_pair"
      else:
          paired_filter = ""
      filter_string = base_filter.format(paired_filter=paired_filter)
      sambamba = config_utils.get_program("sambamba", config)
      num_cores = dd.get_num_cores(data)
      with file_transaction(out_file) as tx_out_file:
          cmd = ('{sambamba} view -h{type_flag} '
                 '--nthreads {num_cores} '
                 '-f bam {bed_cmd} '
                 '{filter_string} '
                 '{align_file} '
                 '> {tx_out_file}')
          message = "Removing multimapped reads from %s." % align_file
          do.run(cmd.format(**locals()), message)
      bam.index(out_file, config)
      return out_file
docs: Filtering a BWA alignment file for uniquely mapped reads, from here:
      https://bioinformatics.stackexchange.com/questions/508/obtaining-uniquely-mapped-reads-from-bwa-mem-alignment