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
- 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
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.
- 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.
See [[the BGEN library API]].