The BGEN reference implementation

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

Releases

See the page on BGEN library [[Releases]].

Information on the BGEN format

• See the BGEN specification for full details of the format.
• Missing data in BGEN
• How much accuracy do I need
• BGEN in the UK Biobank

Compiling and using BGEN

• See the repository page for details on downloading and compiling the bgen code.
• Troubleshooting compilation

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]].