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.

References:

Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnology (2013) Mar; 31(3)213-9
• Paper

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

• MuTect Homepage
• MuTect Discussion Forum

• Module Name: muTect (see the modules page for more information)
• Singlethreaded
• Environment variables set
  • MUTECT_JAR - full path to the mutect jar
  • MUTECT_JARPATH - path to the directory containing the mutect jar
• Reference data in /fdb/muTect/

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.

• --memory memory allocated (default = 2gb)
• --tmpdir tmpdir location (default = /lscratch)

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.

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 ~]$

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

#!/bin/bash
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=#] muTect.sh