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.
How to Use
MuTect uses environment modules. Typemodule load muTect
at the prompt. Then typemuTect
Two extra options have been added to allow for memory allocation and tempdir location.
- --memory memory allocated (default = 2gb)
- --tmpdir tmpdir location (default = /scratch/$USER/muTect)
By default, muTect uses 2gb of memory. To allocate 20gb of memory, include --memory 20g on the commandline.
NOTE 1: muTect does NOT work with java v1.7. Instead, make sure to either rely on the java version set by the muTect module, or only use java v1.6.module load java/1.6.0
NOTE 2: 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.
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.
A typical commandline would be as follows:muTect -m 8g --analysis_type MuTect \ --reference_sequence /fdb/muTect/Homo_sapiens_assembly19.fasta \ --dbsnp /fdb/muTect/dbsnp_132_b37.leftAligned.vcf \ --cosmic /fdb/muTect/hg19_cosmic_v54_120711.vcf \ --intervals 17:7577100-7577200 \ --input_file:normal Normal.cleaned.bam \ --input_file:tumor Tumor.cleaned.bam \ --out example.call_stats.txt \ --coverage_file example.coverage.wig.txt