Definition of outlier loci in Lositan

Question

[katrin.heer]

For outlier detection in our SNP data we have been using Lositan and have a question
regarding the definition of outlier loci:
In our graphs we find most loci defined as outliers in the area with very low heterozygosity were no envelop is defined (in the default output this area is just a straight line, when we created plots in R we used the output files conf-interv)). Nevertheless, loci in that are said to be outliers - how reliable is this approach and on what grounds are the
outliers defined?

We would be grateful for any suggestions how to deal with this.

Best,

Katrin

Answer 1

[tiagoantao]

It seems that this result is completely artefactual. That is, it is a problem with the underlying coalescent model. I would not trust LOSITAN on this, at all.