What is allele harmonization?

Allele harmonization ensures that a SNP’s effect on the exposure and its effect on the outcome must correspond to the same allele. This is challenging with palindromic SNPs.

There are three options to harmonize the data:

  1. Assume that all alleles are on the forward strand (5’ to 3’);
  2. Use the allele frequency information to infer which is the forward strand allele (effect allele);
  3. Remove all palindromic SNPs for which the direction is impossible to infer.