How to change variant IDs in plink files?
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Entering edit mode
13 months ago
kraincimages ▴ 20

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 • 1.6k views
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3
Entering edit mode
13 months ago

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.

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