How to convert bgen data files to PLINK format

Question

[bha]

I have sequence data which is in .bgen format .

Wanted to convert this into PLINK format. Any suggestion what's the best way to do this?

Answer 1

[zx8754]

Why convert? plink accepts bgen format as input, see:

• http://www.cog-genomics.org/plink/1.9/input#oxford

[bha]

I tried this: plink2 --bgen data.chr22.bgen --make-bed --out ex22 But got this error message:

Error: .bgen file does not contain sample IDs, and no .sample file was specified.

what am i missing in command?

[zx8754]

Error message is clear, you are missing sample file --sample [filename].