I'm working with a panel of 13K SNPs generated using a modified ddRAD library prep. The two "populations" are survivors vs dead of the same inbred individuals. I'm trying to use Lositan to test for outlier loci between these two groups but as you can see below, I'm getting a crazy plot for He vs Fst. I don't think it reflects biology. So I'm wondering if ...
... there is a problem with the SNPs themselves? The samples are from a salmonid, so I've trying to deal with the problems posed by paralogy.
... there is a problem with Lositan and how its calculating Fst or He? Or with the genepop input?
Any insight would be appreciated!