code: def _make_ignore_file(work_dir, ref_file, ignore_file, impute_file):
      
      gl_file = os.path.join(work_dir, "gender_loci.txt")
      chroms = set([])
      with open(impute_file) as in_handle:
          for line in in_handle:
              chrom = line.split()[0]
              chroms.add(chrom)
              if not chrom.startswith("chr"):
                  chroms.add("chr%s" % chrom)
      with open(ignore_file, "w") as out_handle:
          for contig in ref.file_contigs(ref_file):
              if contig.name not in chroms:
                  out_handle.write("%s\n" % contig.name)
      with open(gl_file, "w") as out_handle:
          for contig in ref.file_contigs(ref_file):
              if contig.name in ["Y", "chrY"]:
                  # From https://github.com/cancerit/cgpBattenberg/blob/dev/perl/share/gender/GRCh37d5_Y.loci
                  positions = [2934912, 4546684, 4549638, 4550107]
                  for pos in positions:
                      out_handle.write("%s\t%s\n" % (contig.name, pos))
      return ignore_file, gl_file
docs: Create input files with chromosomes to ignore and gender loci.