mitopy is a command-line toolkit to perform identification and analysis of short mitochondrial variants. The mitochondrial variant detection is based on GATK best practices. Functionality for analysis of detected variants includes annotation, visualization, haplogroup identification and coverage calculation. For further information, please see documentation.
The preferred way of running mitopy is through Docker. Please install Docker and Docker Compose on your system.
Clone the repository:
git clone https://github.com/bendda/mitopy
Start the Docker container in interactive mode:
cd mitopy
docker compose run mitopy
Run the whole mitopy pipeline on example data:
mitopy run-pipeline example_data/NA12878_20k_hg38.bam -o example_data/outputs
To run the analysis on your files, please add them to data/ directory.
NOTE
It is important to add custom data required for analysis to data/ directory, since the data/ directory is mounted to Docker container (for further information, see Docker Volumes).
To run a suite of mitopy tests, run following command (in the cloned mitopy directory):
docker compose run test