MutaGene is a Python package for analyzing mutations and mutational processes in cancer. It provides command-line tools that complement the MutaGene website.
Requires Python 3.10+.
pip install mutageneFor the local web interface:
pip install mutagene[web]| Command | Description |
|---|---|
mutagene fetch |
Download genomes, cancer datasets, and cohorts from remote sources |
mutagene profile |
Create mutational profiles from samples (MAF/VCF input) |
mutagene rank |
Rank mutations by driver status using expected mutability |
mutagene motif |
Test samples for presence of mutational motifs |
mutagene signature |
Decompose profiles into known mutational signatures |
mutagene serve |
Start local web server for interactive analysis |
Use mutagene <command> --help for detailed usage of each subcommand.
# Download a genome assembly and the precalculated cohorts
mutagene fetch genome hg19
mutagene fetch cohorts
# Create a mutational profile
mutagene profile -i sample.maf -g hg19 -o profile.tsv
# List the available cohorts, then rank driver mutations against one
mutagene rank -c
mutagene rank -i sample.maf -g hg19 --cohort Lung_Adenocarcinoma
# Search for mutational motifs
mutagene motif -i sample.maf -g hg19 --motif 'C[C>T]G'
# Decompose into COSMIC signatures
mutagene signature -i sample.maf -g hg19 -s COSMICv2
# Start the web interface
mutagene serveEvery subcommand accepts --params-out FILE to record the parameters of a run,
and --params-in FILE to replay it:
mutagene profile -i sample.maf -g hg19 -o profile.tsv --params-out run.json
mutagene profile --params-in run.json -o rerun.tsvThe genome assembly must match the coordinates in your input file. Run with -v
to see how many reference alleles disagree with the assembly; a large share
means the wrong one was chosen.
If you use MutaGene, please cite:
Goncearenco A, Rager SL, Li M, Sang Q, Rogozin IB, Panchenko AR. Exploring background mutational processes to decipher cancer genetic heterogeneity. Nucleic Acids Res. 2017; 45(W1):W514-W522. https://doi.org/10.1093/nar/gkx367
For the driver ranking method (mutagene rank):
Brown AL, Li M, Goncearenco A, Panchenko AR. Finding driver mutations in cancer: Elucidating the role of background mutational processes. PLOS Computational Biology 2019; 15(4): e1006981. https://doi.org/10.1371/journal.pcbi.1006981