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

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.

snp plink2
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updated by Santosh Anand Santosh Anand • written by sjunlee89 • sjunlee89

1 answer

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

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written by Santosh Anand Santosh Anand

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.

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written by Kevin Blighe Kevin Blighe

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