Hi there,

I have a question regarding Hardy-Weinberg equilibrium and GWAS.

As I understand it, genotyping errors can result in genotype frequencies that deviate significantly from HWE, which is why we use HWE as a QC filter for GWAS.

I am working with a livestock species that is under heavy selection, so I would expect a large deviation from HWE.

Other livestock papers I've read do remove SNPs that deviate from HWE, but they never justify the cut-off statistic. Some say P < 0.05, some P < 0.001, others P < 10^-6.

Can anyone offer any wisdom, or point me in the direction of a resource that will help me make a decision?

Any help would be much appreciated.

Kind regards