Adding rs# in bim bed fam file & separating 1 column chr:bp_a1_a2 to 4 columns

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Muhammad Jabbar

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Jul 3, 2021, 6:40:35 AM7/3/21

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Hi,

I have my base data of .bim (fam bed also there) with column chr:bp_a1_a2 format, there is no rs# column. I make a sample GWAS and found corresponding rs# online from this link Kaviar - known variants in the human genome, release 160204 (systemsbiology.net) and added to sample GWAS file. Just few BP does not exists or does not have rs#.

My question is:

I need to add 1 column as rs# and separate the 1 columns chr:bp_a1_a2 to 4 columns like chr bp a1 a2 in my base files of .bim .fam .bed ? is there any way to do so?

I see some comments to deal it with --set-all-var-ids , what parameter it need? does i have to attach some file after this command?

my command be like..

add_rs = paste0("plink2 --bfile ",dataname , " --set-all-var-ids") #what parameter to add here