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The BGEN reference implementation

This wiki describes the bgen reference implementation along with useful tools.


See the page on BGEN library Releases.

Information on the BGEN format

Compiling and using BGEN

Information on the bgenix index format

See The bgenix index file format.

Tools for working with BGEN files

Included in this repository:

  • bgenix is a tool for efficient queries in BGEN files (included in this repository).
  • cat-bgen a utility for efficiently concatenating BGEN files, e.g. imputation chunks. (Included in this repository)
  • edit-bgen is a utility for editing BGEN metadata.
  • rbgen is an R package for reading data from BGEN files.

Available elsewhere:

  • qctool v2 is under development, and can convert between all flavours of BGEN and other file formats including GEN and VCF.
  • qctool v1 supports BGEN v1.1.
  • plink 1.9 supports BGEN v1.1.
  • mega2 supports BGEN v1.1 and v1.2.

API documentation

See the BGEN library API.