code: def filter_vcf_by_sex(vcf_file, items):
      
      out_file = "%s-ploidyfix%s" % utils.splitext_plus(vcf_file)
      if not utils.file_exists(out_file):
          genders = list(_configured_genders(items))
          is_female = len(genders) == 1 and genders[0] and genders[0] in ["female", "f"]
          if is_female:
              orig_out_file = out_file
              out_file = orig_out_file.replace(".vcf.gz", ".vcf")
              with file_transaction(items[0], out_file) as tx_out_file:
                  with open(tx_out_file, "w") as out_handle:
                      with utils.open_gzipsafe(vcf_file) as in_handle:
                          for line in in_handle:
                              if line.startswith("#"):
                                  out_handle.write(line)
                              else:
                                  chrom = chromosome_special_cases(line.split("\t"))
                                  if chrom != "Y":
                                      out_handle.write(line)
              if orig_out_file.endswith(".gz"):
                  out_file = vcfutils.bgzip_and_index(out_file, items[0]["config"])
          else:
              out_file = vcf_file
      return out_file
docs: Post-filter a single sample VCF, handling sex chromosomes.
  
      Removes Y chromosomes from batches with all female samples.