def run_mutect(job, normal_bam, normal_bai, tumor_bam, tumor_bai, ref, ref_dict, fai, cosmic, dbsnp):
work_dir = job.fileStore.getLocalTempDir()<EOL>file_ids = [normal_bam, normal_bai, tumor_bam, tumor_bai, ref, fai, ref_dict, cosmic, dbsnp]<EOL>file_names = ['<STR_LIT>', '<STR_LIT>', '<STR_LIT>', '<STR_LIT>', '<STR_LIT>',<EOL>'<STR_LIT>', '<STR_LIT>', '<STR_LIT>', '<STR_LIT>']<EOL>for file_store_id, name in zip(file_ids, file_names):<EOL><INDENT>job.fileStore.readGlobalFile(file_store_id, os.path.join(work_dir, name))<EOL><DEDENT>parameters = ['<STR_LIT>', '<STR_LIT>',<EOL>'<STR_LIT>', '<STR_LIT>',<EOL>'<STR_LIT>', '<STR_LIT>',<EOL>'<STR_LIT>', '<STR_LIT>',<EOL>'<STR_LIT>', '<STR_LIT>',<EOL>'<STR_LIT>', '<STR_LIT>',<EOL>'<STR_LIT>', str(<NUM_LIT:10>),  <EOL>'<STR_LIT>', str(<NUM_LIT>),  <EOL>'<STR_LIT>', '<STR_LIT>',<EOL>'<STR_LIT>', '<STR_LIT>',<EOL>'<STR_LIT>', '<STR_LIT>']<EOL>dockerCall(job=job, workDir=work_dir, parameters=parameters,<EOL>tool='<STR_LIT>')<EOL>output_file_names = ['<STR_LIT>', '<STR_LIT>', '<STR_LIT>']<EOL>output_file_paths = [os.path.join(work_dir, x) for x in output_file_names]<EOL>tarball_files('<STR_LIT>', file_paths=output_file_paths, output_dir=work_dir)<EOL>return job.fileStore.writeGlobalFile(os.path.join(work_dir, '<STR_LIT>'))<EOL>
Calls MuTect to perform variant analysis

:param JobFunctionWrappingJob job: passed automatically by Toil
:param str normal_bam: Normal BAM FileStoreID
:param str normal_bai: Normal BAM index FileStoreID
:param str tumor_bam: Tumor BAM FileStoreID
:param str tumor_bai: Tumor BAM Index FileStoreID
:param str ref: Reference genome FileStoreID
:param str ref_dict: Reference dictionary FileStoreID
:param str fai: Reference index FileStoreID
:param str cosmic: Cosmic VCF FileStoreID
:param str dbsnp: DBSNP VCF FileStoreID
:return: MuTect output (tarball) FileStoreID
:rtype: str