def merge_phlat_calls(job, tumor_phlat, normal_phlat, rna_phlat):
    job.fileStore.logToMaster('Merging Phlat calls')
    work_dir = job.fileStore.getLocalTempDir()
    input_files = {
        'tumor_dna': tumor_phlat,
        'normal_dna': normal_phlat,
        'tumor_rna': rna_phlat}
    input_files = get_files_from_filestore(job, input_files, work_dir)
    with open(input_files['tumor_dna'], 'r') as td_file, \
            open(input_files['normal_dna'], 'r') as nd_file, \
            open(input_files['tumor_rna'], 'r') as tr_file:
        mhc_alleles = {'HLA_A': [], 'HLA_B': [], 'HLA_C': [], 'HLA_DPA': [], 'HLA_DQA': [],
                       'HLA_DPB': [], 'HLA_DQB': [], 'HLA_DRB': []}
        for phlatfile in td_file, nd_file, tr_file:
            mhc_alleles = parse_phlat_file(phlatfile, mhc_alleles)
    with open(os.path.join(work_dir, 'mhci_alleles.list'), 'w') as mhci_file, \
            open(os.path.join(work_dir, 'mhcii_alleles.list'), 'w') as mhcii_file:
        for mhci_group in ['HLA_A', 'HLA_B', 'HLA_C']:
            mpa = most_probable_alleles(mhc_alleles[mhci_group])
            print('\n'.join([''.join(['HLA-', x]) for x in mpa]), file=mhci_file)
        drb_mpa = most_probable_alleles(mhc_alleles['HLA_DRB'])
        print('\n'.join([''.join(['HLA-', x]) for x in drb_mpa]), file=mhcii_file)
        dqa_mpa = most_probable_alleles(mhc_alleles['HLA_DQA'])
        dqb_mpa = most_probable_alleles(mhc_alleles['HLA_DQB'])
        for dqa_allele in dqa_mpa:
            for dqb_allele in dqb_mpa:
                print(''.join(['HLA-', dqa_allele, '/', dqb_allele]), file=mhcii_file)
    output_files = defaultdict()
    for allele_file in ['mhci_alleles.list', 'mhcii_alleles.list']:
        output_files[allele_file] = job.fileStore.writeGlobalFile(os.path.join(work_dir,
                                                                               allele_file))
    return output_files