Bioinformatics method to identify individual driver mutations.

INSTALL

Create a new Anaconda python environment with all the required dependencies

$ conda create -c bioconda -c bbglab -n oncodrivemut python=3.5 numpy=1.11 pandas=0.17 colorama=0.3 ago requests=2.11 pytabix=0.1 itab=0.9 bgconfig=0.3 $ source activate oncodrivemut $ pip install oncodrivemut-1.0.0.tar.gz --no-deps

The first time that you run OncodriveMUT it will download all the required datasets using bgdata (https://bitbucket.org/bgframework/bgdata)

by default bgdata downloads all the files at ~/.bgdata check the documentation if you can to change this behaviour

$ oncodrivemut -h usage: oncodrivemut [-h] -i INPUT_FILE [-o OUTPUT_FOLDER] [-t TUMOR_TYPE] [-c CONFIG_FILE] [-s SAMPLE] [--force] [--debug] [--extended] optional arguments: -h, --help show this help message and exit -i INPUT_FILE, --input INPUT_FILE Variants file -o OUTPUT_FOLDER, --output OUTPUT_FOLDER Output folder. Default to regions file name without extensions. -t TUMOR_TYPE, --tumor TUMOR_TYPE Specify the tumor type of the sample(s) under analysis -c CONFIG_FILE, --config CONFIG_FILE Configuration file. Default to 'oncodrivemut.conf' in the current folder if exists or to ~/.bbglab/oncodrivemut.conf if not. -s SAMPLE, --sample SAMPLE Default identifier of the sample --force Run the commands and overwrite results although output files already exist --debug Show more progress details --extended Computational expensive metrics are also calculated for non coding mutations