This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to change variant IDs in plink files?

Hi all

Question about changing IDs... I have two plink files that I need to merge but they have different ID formats, one has chr_pos_ref_alt and one has chr_pos.

I would like to change chr_pos_ref_alt into chr_pos but I am struggling to find a way to do this, does anyone know of a way to do this?

Thanks!

plink gnomad id
• 9,962 views • link
updated by zx8754 zx8754 • written by kraincimages • kraincimages

1 answer

The simplest way to do this is to use plink 2.0's --set-all-var-ids flag:

plink2 --bfile ... --set-all-var-ids @_# --make-bed ...

This is also pretty easy to do with a shell script operating on the .bim file.

• 0 views • link
written by chrchang523 chrchang523

Log in to answer this question.

More posts like this