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

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.

plink liftover update rsid
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updated by Samah • Samah • written by hi.there • hi.there

1 answer

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

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written by Samah • Samah

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