A bgen file format reader.
Bgen is a file format for storing large genetic datasets. It supports both unphased genotypes and phased haplotype data with variable ploidy and number of alleles. It was designed to provides a compact data representation without sacrificing variant access performance.
This python package is a wrapper around the bgen library, a low-memory footprint reader that efficiently reads bgen files. It fully supports the bgen format specifications: 1.2 and 1.3; as well as their optional compressed formats.
It can be installed via conda
conda install -c conda-forge bgen-readerOr via pip
pip install bgen-readerPlease, refer to https://bgen-reader.readthedocs.io.
This means that bgen C library is not installed (or could not be found). Please, follow the instructions in https://github.com/limix/bgen to install it, and try installing bgen-reader again.
If you encounter any issue, please, submit it.
This project is licensed under the MIT License.