I am trying to run an analysis of SMR analysis of two molecular traits with methylation and expression. However, I always get a high percentage of allele differences between pairwise data sets (including the outcome eQTL summary data, the exposure eQTL summary data and the LD reference data)
This is the ERROR: 370895 SNPs (73.16% > 5.00%) with allele frequency differences > 0.20 between any pair of the data sets are excluded from the analysis. ERROR: the analysis stopped because more than 5.00% of the SNPs were removed by the allele frequency difference check. You can change the proportion threshold by the flag --diff-freq-prop
However, my expression and methylation have the same allele frequency, they are from the same individuals and when I check the frequency of my LD (1000 Genomes phase3 CEU) using plink: plink --bfile my1000GP3_CEU --freq, and check the differences only a few SNPs have 0.20 differences, how the program calculate the differences??