CAVA v1.2.3 README ================== 1 INTRODUCTION -------------- 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. 2 PUBLICATION ------------- 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). 3 DEPENDENCIES -------------- To install and run CAVA v1.2.3 you will need the following dependencies installed: - Python 2.7.9 or later (Python2 series) - GCC and GNU make - virtualenv If your system is missing GCC and GNU make, these can be installed as follows: 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: sudo apt-get install build-essential If not already installed on your system, virtualenv can be set up by: pip install virtualenv 4 INSTALLATION ON LINUX OR MAC ------------------------------ CAVA v1.2.3 can be downloaded from https://github.com/RahmanTeam/CAVA/releases/tag/v1.2.3 in either .zip or .tar.gz format. To unpack these run one of the following commands: unzip CAVA-1.2.3.zip or: tar -xvzf CAVA-1.2.3.tar.gz and then you can install CAVA with the following command from the CAVA-1.2.3 directory: ./install.sh CAVA 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-1.2.3 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. 5 RUNNING CAVA -------------- CAVA can be run with the following simple command: CAVA-1.2.3/cava -c config.txt -i input.vcf -o output It 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). 6 DOCUMENTATION --------------- See CAVA-v1.2,3_doc.pdf for detailed documentation and examples. 7 LICENCE --------- CAVA is released under MIT licence (see the LICENCE file).