Population comparison of allele frequencies pool-seq data

[salejandro]

Dear authors,

How can I calculate the LR to compare allele frequencies between pooled samples (i.e., equation 8 in Michael Lynch, Darius Bost, Sade Wilson, Takahiro Maruki, Scott Harrison, Population-Genetic Inference from Pooled-Sequencing Data, Genome Biology and Evolution , Volume 6, Issue 5, May 2014, Pages 1210–1218).

I have tried the -p flag in the "mapgd pool" command, but I get the same result in the *.pol file, without any extra information about the allele frequency comparison.

Thanks.

A.