plink2 extract subset of samples from .bgen file
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?
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chrchang523
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UMen •
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written
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UMen •
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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.
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