I would like to test to see if a list of variants are in HWE
Say I have 100 loci with biallelic (AA/Aa/aa) genotypes for 1,000 samples. I would like to test that on average are the alleles in HWE.
Do I calculate a chi-squared statistic across each allele and then take the mean/median Chi-Sq stat to find the Pvalue?
I am assuming that each region is independent of each other (no linkage)