I have run a meta-analysis using METAL, and I have an output file (ending in ".tbl") including an "Effect" column and an "Allele1" and "Allele2". I would like to compare the effect column of this analysis to another dataset, but in order to do so I need to align the betas depending on which allele the effects refer to. I was wondering if I can assume that the effect is computed for the allele specified in the "Allele1" field.
The Wiki documentation for METAL talks about the first study included in the meta-analysis being used as the reference for the alleles, so if I am understanding this correctly the "Effect" is expressed in reference to "Allele1". If this is not the case, how can I find the allele that is used as the effect allele?
Thank you very much for all your help,