interpretation

[Afreen89]

Hello,

The sumstats I have has effect allele and other allele, could you specify if you are taking reference as effect allele or the other allele in the code here:

I am new in the field, its confusing for me between effect allele, reference allele, major allele and A1. I am giving it a sumstats for a few phenotypes, and I have effect and other allele. I am just renaming the columns to match the code.

[sgagliano]

Hello. Thanks for the question. The alternate allele, A2 (i.e.non-reference allele) is the effect allele.

Hope this helps!