Updating hg 18 .bim file with lifted .map and .bed file

Question

[hi.there]

Hello,

I am trying to update rsids in an hg18 .bim file with an hg38.bed and hg38.map file. I've tried the following: system("./plink --file plink_hg38 --make-just-bim --out newBim --allow-extra-chr")

but got the error: Error: Failed to open plink_hg38.ped.

I see no commands to make a .ped file so I am curious if any of you know how to make a new .fam, .ped and .bim file. Thank you.

Answer 1

[Samah]

plink binary files are .bed, .bim and .fam and you can read them through --bfile option, while to plink MAP format (.ped and .fam ) can be read by --file option: to convert from binary to MAP format use: plink --bfile hg38 --recode --out outputfile to make new binary files use --make-bed option