How to convert PLINK data files to bgen and bgen.bgi files?

Question

[rednalf]

For a specific script, I need genotyping data in .bgen and .bgen.bgi format. How can I obtain those formats starting from PLINK data files?

Answer 1

[chrchang523]

With PLINK 2.0,

plink2 --bfile ... --export bgen-1.2 --out ...

can be used to create the bgen file (replace "1.2" with "1.1" or "1.3" if you want a different format version). bgenix (https://bitbucket.org/gavinband/bgen/wiki/bgenix ) can then be used to construct the .bgen.bgi index.