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

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