Changing the sample IDs of a bed/bim/fam PLINK fileset

Question

[Arta]

Hi everyone,

I am working with a genotype set that is not identified with the samples IDs that I want. However, I do have a lookup table which I can use in R to get the right identification when I need it.

My question is: how do I fully replace the IDs using PLINK so that I don't have to cross-reference with R everytime?

--update-ids is all I have so far

Thank you

[4galaxy77]

Why not just use R to replace the IDs in the .fam file - you would only have to do this once and then you can use the correct IDs. Unless I misunderstand your question.

[4galaxy77]

Sorry @Arta, I deleted my comment. But no, it wouldn't matter since the names aren't stored in the .bed file - the names are stored in order in the .fam, so you can change them, as long as you keep the lines in the same order.