Just had a very simple question regarding the use of the A1 and A2 alleles. From the manual it says that,
Columns are SNP, the coded allele (also called the effect allele or the reference allele), the other allele (also called the alternative allele), frequency of the effect allele, effect size, standard error, p-value and sample size. The headers are not keywords and will be omitted by the program. Important: “A1” needs to be the effect allele with “A2” being the other allele and “freq” needs to be the frequency of “A1”.
This means that A1 is the effect allele, which is in line with PLINK correct? If I recall correctly, PLINK refers A1 as the minor allele and is also the effect that is being modeled.
I wanted to clarify because we are using SNPTEST which uses the allele_B as the effect allele. So if we would like to keep everything concordant with SMR, we will have the change the allele_B output to being A1. Is that correct or am I interpreting that incorrectly.