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How to convert bgen data files to PLINK format

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?

plink software bgen
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updated by Biostar Biostar • written by bha bha

1 answer

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

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written by zx8754 zx8754

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?

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written by bha bha

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

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written by zx8754 zx8754

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