Biowulf High Performance Computing at the NIH
muTect on Biowulf

MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.


NOTE: MuTect has been merged into the most recent versions of GATK, and is no longer supported as a separate application. Please see for information on using GATK.

Important Notes

NOTE: muTect uses code base from GATK, and therefore has many of the same options. One option, -nt or --num_threads DOES NOT work properly. DO NOT use this option.

MuTect requires two BAM input files, one for normal tissues, the other for the tumor tissue. MuTect outputs a wiggle format coverage file. An additional wiggle file can be generated to display observed depth.

Two extra options have been added to allow for memory allocation and temporary file directory.

By default, muTect uses 2gb of memory. To allocate 5gb of memory, include --memory 5g on the commandline.

MuTect takes as parameters database files, depending on the build of your alignments and which dbSNP version you are using. These files are located in /fdb/muTect.

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. For example:

module load muTect
muTect --memory 8g --analysis_type MuTect \
--reference_sequence /fdb/muTect/ucsc.hg19.fasta \
--dbsnp              /fdb/muTect/dbsnp_137.hg19.vcf \
--cosmic             /fdb/muTect/cosmic_v67.hg19.vcf \
--input_file:normal /full/path/to/Normal.cleaned.bam \
--input_file:tumor /full/path/to/Tumor.cleaned.bam \
--out /full/path/to/example.call_stats.txt \ 
--coverage_file /full/path/to/example.coverage.wig.txt

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#]