code: def run_mutation_aggregator(job, fusion_output, radia_output, mutect_output, indel_output,
                              univ_options):
      job.fileStore.logToMaster('Aggregating mutations for %s' % univ_options['patient'])
      work_dir = job.fileStore.getLocalTempDir()
      input_files = {
          'mutect.vcf': mutect_output,
          'radia.vcf': radia_output['radia_parsed_filter_passing_calls.vcf'],
          'indel.vcf': indel_output,
          'fusion.vcf': fusion_output}
      input_files = get_files_from_filestore(job, input_files, work_dir, docker=False)
      input_files.pop('indel.vcf')
      input_files.pop('fusion.vcf')
      vcf_file = defaultdict()
      mutcallers = input_files.keys()
      with open(''.join([work_dir, '/', univ_options['patient'], '_merged_mutations.vcf']),
                'w') as merged_mut_file:
          for mut_caller in mutcallers:
              caller = mut_caller.rstrip('.vcf')
              vcf_file[caller] = defaultdict()
              with open(input_files[mut_caller], 'r') as mutfile:
                  for line in mutfile:
                      if line.startswith('
                          if caller == 'radia':
                              print(line.strip(), file=merged_mut_file)
                          continue
                      line = line.strip().split()
                      vcf_file[caller][(line[0], line[1], line[3], line[4])] = line
      merge_vcfs(vcf_file, merged_mut_file.name)
      export_results(merged_mut_file.name, univ_options)
      output_file = job.fileStore.writeGlobalFile(merged_mut_file.name)
      return output_file