Changing from "rs" to "chr_pos_ref_alt"

Question

[Karan]

I'm attempting to change my SNP ids (in my bim file) from "rs_________" to "chr_pos_ref_alt" but am having some trouble.

Can someone provide some guidance? What awk scripts could I use?

EDIT: basically trying to switch from "rs11260745" to "1_24088128_G_A"

Answer 1

[chrchang523]

plink 2.0's --set-all-var-ids flag provides one way to do this.

[Karan]

awesome, thank you!

[Helix]

That's a very cool feature. Can I convert from CHR_POS to rsIDs by PLINK, vice versa?

Answer 2

[Ram]

Use bcftools annotate -I. Your requirement is the exact example given in the manual.

[Karan]

perfect, thanks for linking the manual!