JonJala
Inconsistent allele
Hi, I am running a multivariate analysis, but I discovered MTAG is dropping a whole lot of SNPs due to inconsistent allele. Is there a flag to include to retain this inconsistent allele, or a method to go round this.
Dropped 25464668 SNPs due to inconsistent allele pairs from phenotype 2. Dropped 1896135 SNPs due to inconsistent allele pairs from phenotype 3
So that filter checks to make sure that the major/minor allele pairs are consistent across phenotypes. It looks like phenotype 1 is used as the reference / ground truth there, and each of the other phenotypes are checked to make sure A1/A2 is either the same or swapped, and anything else is dropped. MTAG results wouldn't be very useful if those weren't kept consistent.
