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Plink extract SNPs from .ped file using ID

Hi,

I have a .ped file containing data from 3 groups of population. I have checked the documentation of the PLINK for extracting the subset of data from the PLINK files, but couldn't find the way to extract data based on ID(s). Could you please provide an idea on how to achieve this?

plink gwas snp
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updated by Ram 4.5K • | written by deepue 16

1 answer

--keep: https://www.cog-genomics.org/plink2/filter#indiv

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updated by Ram 4.5K • | written by alesssia 58

I tried the below command but it didn't work. Did I miss anything?

plink --file combined_maternal --extract ../pop1_IDs.txt --make-bed --out ../pop1
• 0 views • link
updated by Ram 4.5K • | written by deepue 16

You should use --keep, not --extract. From the linked page:

--keep accepts a space/tab-delimited text file with family IDs in the first column and within-family IDs in the second column, and removes all unlisted samples from the current analysis.

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updated by Ram 4.5K • | written by alesssia 58

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