How to determine effect allele of GWAS meta-analysis

Question

[helen]

Hi all,

I have performed meta-analysis from two GWAS summary statistics using METAL and Metasoft. Metasoft gives you output from different statistic models (e.g., fixed effect, random effect), but it lacks columns like effect allele, non-effect allele, and direction of each study. My question is how does meta-analysis determine the effect allele if the allele is different across each input summary data? How do I add this column to my Metasoft output since the "effect allele" column is required in the following functional annotation tool (I use FUMA)?

Any suggestions would be appreciated!

[Som]

Hello @helen Did you find the solution to this question? I'm having the same issue.

Thank you

Answer 1

[hongbo919]

I also have the question. METAL reported the effect allele and direction. However, some direction were opposite to the original effect value, which may be caused by the allele flipping. Meta-Analysis effect size is not in the same direction as GWAS effect sizes.