Question: What is the meaning of REF, ALT, A1 on the logistic analysis (--glm) using Plink2?
0
gravatar for sjunlee89
2.0 years ago by
sjunlee890
sjunlee890 wrote:

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 • 1.2k views
ADD COMMENTlink modified 2.0 years ago by Santosh Anand5.2k • written 2.0 years ago by sjunlee890
1
gravatar for Santosh Anand
2.0 years ago by
Santosh Anand5.2k
Santosh Anand5.2k wrote:

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

ADD COMMENTlink written 2.0 years ago by Santosh Anand5.2k

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.

ADD REPLYlink written 2.0 years ago by Kevin Blighe69k
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