plink2 extract subset of samples from .bgen file

Question

[UMen]

Hi Biostars,

I try to extract a subset of samples from a .bgen file using plink2. Output format should also be .bgen.
Searched the manpages without success. Can anybody help me?

Answer 1

[chrchang523]

plink2 \
  --bgen <.bgen filename> ref-last \
  --sample <.sample filename> \
  --keep <file with sample IDs to keep> \
  --export bgen-1.3 \
  --out <output filename prefix>

Note that this only preserves dosages, not genotype probabilities. If you care about preserving the raw probabilities in the .bgen file, you cannot use plink2.