Plink: --keep flag
I want to subset my genotype files (ped and map) to get the data for a few samples only. I used the --keep flag from plink to do the same.
Command used : plink --file <filename> --keep keep_individuals.txt --make-bed --out data_keep
ERROR : Error: Line 1 of --keep file has fewer tokens than expected.
My --keep file (keep_individuals.txt) looks like this with the sample names:
VD19843994GD QG64443798DS RH77483094DT LK12525917MG SC30880954YF
Can somebody please tell me how should I work around this error?
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chrchang523
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Swetaleena •
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Swetaleena •
1 answer
.ped files have two-part sample IDs ("FID" and "IID"). When using plink 1.x, your --keep file must have two columns, where the first column has FIDs and the second column has IIDs.
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