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 Former User of DNAx Community_10 19 June 2023 00:00 2 comments Comments 2 comments Sort by Date Votes George F UKB Community team Data Analyst 20 June 2023 10:42 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.txtplink --bfile ukb22418_cMT_b0_v2 --extract extract_SNPs.txt --make-bed --out output 0 Former User of DNAx Community_35 13 August 2023 14:57 Can you please suggest, how we can run this command using dx or R studio? 0 Please sign in to leave a comment.
Comments
2 comments
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
Can you please suggest, how we can run this command using dx or R studio?
Please sign in to leave a comment.