Question: same rsID but swapped alleles for A1 and A2 in bivariate analysis

[yunkaig]

Hi,

As per the title, this is a question rather than an 'issue'.

I am running MiXeR v1.3 with Singularity for a bivariate analysis with two GWAS studies. One of the studies (say study A) used the column names Allele1/2 and the other (study B) used EA/OA. Both studies provide rsID.

I found that for the same rsID, chr, and bp, most Allele1 in study A matches the EA in study B, but there is a fraction of SNPs where the Allele1 and Allele2 in study A are swapped compared to study B (i.e. Allele1 in study A now matches OA in study B).

My question is whether this will affect the results of bivariate analysis, or I can safely ignore that.

Thank you