Install

The VAtools suite is written for Linux and Mac OS X. If you are using Windows you will need to set up a Linux environment, for example by using WSL or setting up a virtual machine.

VAtools requires Python 3.10 or above. Before running any installation steps, check the Python version installed on your system:

python --version

pip

Install VAtools using pip:

pip install vatools

You can verify the installation with:

pip show vatools

To upgrade an existing installation:

pip install vatools --upgrade

Docker

A Docker container for VAtools is available on DockerHub using the griffithlab/vatools repo.

docker pull griffithlab/vatools

Run any tool inside the container by passing it as the command. For example:

docker run griffithlab/vatools vcf-readcount-annotator --help

To annotate a VCF with files on your local filesystem, mount the directory containing your data as a volume:

docker run -v /path/to/data:/data griffithlab/vatools \
  vcf-readcount-annotator /data/input.vcf /data/readcounts.tsv DNA \
  -o /data/output.vcf