milescsmith/PLINK_sample_extraction_file.md

Created November 5, 2024 16:18

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Example file for extracting samples from PLINK files

Raw

The manual for PLINK doesn't exactly show what the format is for the file used to extract or remove particular samples.

The easiest format that works that I know of is

#FID IID
4 MDFL|500511
38 LFRR_303939
62 MDFL|500523
94 LFRR_107325
112 CE_541382
118 CH_551587

I don't think the manual is explicit on this, but the FID must match what is in the PLINK files.

Assuming the above is named extract.list, use with the command:

plink2 \
    --bed data.bed \
    --bim data.bim \
    --fam data.fam \
    --keep extract.list \
    --make-pgen \
    --out data_subset

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