Hi All, I have a sequencing data, and I have two minor allele frequencies for a list of SNPs (1000+) by doing SNP call in two softwares. I can see there are difference in the two MAFs for each SNPs. How can I formally test them whether MAF from two softwares are the same or not. I tried paired t-test and wilcoxon paired sign test, they give me opposite answers. Paired t-test's assumption about normal distribution is failed, but wilcoxon test is not powerful. So I don't know what to continue. Any comments is welcome, thank you very much in advance. Jiafen [[alternative HTML version deleted]]