CAVA (Clinical Annotation of VAriants) is a lightweight, fast, flexible and easy-to-use Next Generation Sequencing (NGS) variant annotation tool. It implements a clinical sequencing nomenclature (CSN), a fixed variant annotation consistent with the principles of the Human Genome Variation Society (HGVS) guidelines, optimised for automated clinical variant annotation of NGS data.
CAVA has been extensively tested on exome data and is being used in the Mainstreaming Cancer Genetics (MCG) programme which applies NGS to increase the availability and affordability of clinical testing of cancer predisposition genes.
UPDATE CAVA is no longer being supported by the Rahman Team. This fork is used by the Mayo Clinic to annotate our research and clinical samples.
If you use CAVA, please cite:
Márton Münz, Elise Ruark, Anthony Renwick, Emma Ramsay, Matthew Clarke, Shazia Mahamdallie, Victoria Cloke, Sheila Seal, Ann Strydom, Gerton Lunter, Nazneen Rahman. CSN and CAVA: variant annotation tools for rapid, robust next-generation sequencing analysis in the clinical setting. Genome Medicine 7:76, doi:10.1186/s13073-015-0195-6 (2015).
To install and run CAVA you will need the following dependencies installed:
- Python 3
- GCC and GNU make
- virtualenv
If your system is missing GCC and GNU make, these can be installed as
On a Mac, the easiest way to set them up is to install Xcode Command Line Tools. On a Debian or Ubuntu Linux, they can be set up by installing the build-essential package:
bash sudo apt-get install build-essential
If not already installed on your system, virtualenv can be set up by:
bash pip install virtualenv
git clone https://github.com/Steven-N-Hart/dicom_wsi.git
# optional to checkout release
# e.g. git checkout v.1.2.4
./install.shCAVA uses virtualenv and pip to manage all its extra dependencies, which means that it will not clutter up your system by installing things globally. Everything it installs will go into a sub-directory in the CAVA directory. If you delete CAVA then everything it has installed will also be deleted.
Once the installation script has finished successfully, CAVA is ready for use.
CAVA can be run with the following simple command:
cava -c config.txt -i input.vcf -o outputIt requires three command line arguments: the name of the configuration file (-c), the name of the input file (-i) and the prefix of the output file name (-o).
CAVA is released under MIT licence (see the LICENCE file).