Examples

This page shows examples of running GWA-X.

Test run

We provide some input files to help you get started in the examples repository.
To download the example data:

git clone https://git.ecdf.ed.ac.uk/magung/gwa-x_examples.git
cd gwa-x_examples/

The hapnest/ subdirectory contains a smaller version of HAPNEST synthetic dataset.
You can do a test run using the small files with 100 permutations by running the following command.

python ${GWAX_DIR}/src/main.py \
    --bed hapnest/hapnest_small_ld_qc \
    --phenoFile hapnest/pheno1.phen \
    --bsize 5000 \
    --mperm 100 \
    --out hapnest/test

Replace ${GWAX_DIR} with the GWA-X installation directory.
To use the PGEN files, use --pgen instead of --bed.

This will generate three output files: test.gwax, test.log and test.perm.gwax in the hapnest/ directory.