hardy weinberg equilibrium

Question

[reds.nik]

Hello everybody,

I am trying to figure out which could be a good hardy weinberg equilibrium p-value cutoff for a set of around 40 millions snps coming from whole genome sequencing data of about 2000 people.

Thanks

[Fabio Marroni]

It's a very long topic! To start, you could give a look to this post on Biostars and to this tutorial on data cleaning for GWAS at paragraph 2.4