UKBiobank BGEN Format

Hail appears to currently support BGEN format v1.1 only. Are there any plans to update this to support 1.2 or 1.3? It appears that the upcoming datasets will use 1.2.

thanks very much

Sorry that this question got lost in the shuffle! We intend to support BGEN 1.2 before the release of the next wave of UKBB data in Q2.

Hey -

The next round of UKBB data is almost available (I’m downloading the encrypted bgen files right now, and decryption keys should be distributed sometime in June).

Any updates on bgen 1.2 support? I’m happy to help out if there are things I can do.


Hi Nick,

Hail can import BGEN v1.2 for diploid and unphased data (UK Biobank satisfies this criteria) since the hash f975e69. It is in Hail v0.1. See the documentation for more details.

We are also working on a BGEN v1.2 exporter. This should be ready in the next week or two.


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That’s awesome – thanks!