The coverage_report.py script takes a sambamba file and generates a pdf report that lists any genes that have less than 100% coverage at 30x.
The script can be run using conda or python virtual environments.
cd coverage_test
- Conda:
Create the conda environment
conda env create -f environment.yml
Activate the conda environment
source activate coverage_env
- Python virtual environment:
Activate the python virtual environment
source python_venv/bin/activate
Dependencies are listed in requirements.txt
The coverage_report.py script takes at least one argument to specify the input file. The output file location can also be specified but will be write to coverage_report.pdf as default.
python coverage_report.py -i [input_file] -o [output_file]
- Lucy Mallin
This project is licensed under the MIT License - see the LICENSE.md file for details