What is the meaning of REF, ALT, A1 on the logistic analysis (--glm) using Plink2?

Question

[sjunlee89]

I ran an logistic analysis (--glm) using Plink2 and got some results.

Some SNPs have the same allele between REF and ALT (REF=ALT), others have the same allele between REF and A1 (REF=A1).

As I know, A1 is the minor allele, however, I'm not sure what the REF, ALT, and A1 is exactly.

Please let me know.

Thanks advanced.

Answer 1

[Santosh Anand]

See https://www.cog-genomics.org/plink/2.0/formats

[Kevin Blighe]

I have moved this to an answer because it is all that is needed. sjunlee89, before posting another question, please check the manual for the program that you are using.