I am trying to extract a specific snip from ukb22418_cMT_b0_v2 the mitochondrial hard called chromosome file, The snps are labeled with Affx-, not rs... How do I extract a specific snp, for example Affx-34461959. The usual plink command doesn't work

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  • Comment author
    George F The helpers that keep the community running smoothly. UKB Community team Data Analyst

    You can extract a snp or a list of snps using the --extract option on plink ie:

    grep Affx-3446195 ukb22418_cMT_b0_v2.bim > extract_SNPs.txt

    plink --bfile ukb22418_cMT_b0_v2 --extract extract_SNPs.txt --make-bed --out output

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  • Can you please suggest, how we can run this command using dx or R studio?

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