For command-line users: BGEN support has been implemented in several software packages, click on the links below for more information.
For R users: The rbgen
package can be used to load data directly into R.
For python users: A number of python solutions have been developed, see e.g. the bgen-reader library or the pybgen library.
(Please contact me if your software supports BGEN and you'd like it added to this list.)
For developers: A freely available C++ implementation of the BGEN format is available at code.enkre.net. This repository also contains a number of useful tools:
bgenix
cat-bgen
bgenix
this effectively
enables map/reduce pipelines that operate in parallel on seperate genomic regions.
For example, we have found this useful for joining data into chromosomes after imputing genome-wide.edit-bgen
In addition a set of example files and programs, intended to demonstrate the API, are provided.