code: def _fix_mutect_output(orig_file, config, out_file, is_paired):
      
      out_file_noc = out_file.replace(".vcf.gz", ".vcf")
      none_index = -1
      with file_transaction(config, out_file_noc) as tx_out_file:
          with open_gzipsafe(orig_file) as in_handle:
              with open(tx_out_file, 'w') as out_handle:
                  for line in in_handle:
                      if not is_paired and line.startswith("#CHROM"):
                          parts = line.rstrip().split("\t")
                          none_index = parts.index("none")
                          del parts[none_index]
                          line = "\t".join(parts) + "\n"
                      elif line.startswith("##FORMAT=<ID=FA"):
                          line = line.replace("=FA", "=FREQ")
                      elif not line.startswith("#"):
                          if none_index > 0:
                              parts = line.rstrip().split("\t")
                              del parts[none_index]
                              line = "\t".join(parts) + "\n"
                          line = line.replace("FA", "FREQ")
                      out_handle.write(line)
      return bgzip_and_index(out_file_noc, config)
docs: Adjust MuTect output to match other callers.
  
      - Rename allelic fraction field in mutect output from FA to FREQ to standarize with other tools
      - Remove extra 'none' samples introduced when calling tumor-only samples