Question

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

0

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4.5 years ago

rednalf ▴ 90

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 • 6.1k views

ADD COMMENT • link updated 4.5 years ago by chrchang523 10k • written 4.5 years ago by rednalf ▴ 90

score 5 · Accepted Answer · 2019-11-04

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4.5 years ago

chrchang523 10k

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.

ADD COMMENT • link 4.5 years ago by chrchang523 10k