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

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?

snp genome

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updated 6.8 years ago by chrchang523

• written 6.8 years ago by rednalf

1 answer

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.

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written 6.8 years ago by chrchang523

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