Convert BGEN files to IGD. Uses the limix/bgen library for BGEN reading. Converts to hard calls by taking the allele with the maximum probability (ties are broken by allele order in the file).
Mixed phasedness is not supported. Unphased data is restricted to haploid or diploid. These are not fundamental restrictions, just limitations of the current implementation.
git clone --recursive https://github.com/dcdehaas/bgen2igd.git
cd bgen2igd && mkdir build && cd build
cmake .. -DCMAKE_BUILD_TYPE=Release
make -j
Or use the provide Docker image:
docker build . -t bgen2igd:latest
bgen2igd <bgen filename> <output igd filename>
Or, via docker:
docker run -v $PWD:/pwd/ -it bgen2igd:latest bgen2igd /pwd/your_file.bgen /pwd/your_file.igd