This requires the following 3 steps:

1. Download Data files and SQLite databases

    Data files (54MB)

    SQLite databases (12GB)

    md5sum file

2. Uncompress the downloaded files

    Command:

    Uncompressing the zipped files creates two folders – 'gcndata' and 'gcndb'

3. Set PYTHONPATH and Environment variables

    Set the python path to extracted Varant package location and set environment variables to data     files and SQLite databases. There are multiple ways to do this. These can be set temporarily for     the session in the terminal or stored permanently in the shell configuration files (recommended)     as shown below:

    For cshrc shell

    Edit the .cshrc file located in the home directory (e.g /home/username/.cshrc).
    You can set the PYTHONPATH to varant code base by adding the following to .cshrc -
    setenv PYTHONPATH /path/to/varant
    If the PYTHONPATH was already declared in .cshrc then append the location of varant code base
    as follows -
    setenv PYTHONPATH ${PYTHONPATH}:/path/to/varant
    Set the location of the Varant code base, data files, and databases to the environment variables
    in the .cshrc file as follows:
    setenv GCN /path/to/varant setenv GCN_DATA_DIR /path/to/gcndata setenv GCN_DB_DIR /path/to/gcndb
    Make these variables available to the terminal:
    $ source /home/username/.cshrc

    For bash shell

    Edit the .bashrc file located in the home directory (e.g /home/username/.bashrc).
    You can set the PYTHONPATH to varant code base by adding the following to .bashrc -
    export PYTHONPATH=/path/to/varant
    If the PYTHONPATH was already declared in .bashrc then append the location of varant code base
    as follows -
    export PYTHONPATH=${PYTHONPATH}:/path/to/varant
    Set the location of the Varant code base, data files, and databases to the environment variables
    in the .bashrc file as follows:
    export GCN=/path/to/varant export GCN_DATA_DIR=/path/to/gcndata export GCN_DB_DIR=/path/to/gcndb
    Make these variables available to the terminal:
    $ source /home/username/.bashrc

Varant is now installed and can be run as follows:

1. Go to the Varant 'bin' folder

2. Check the script usage

3. Run the script to annotate the input vcf file

The log file for the run is generated in the same folder as the output.