I would like to compare neutral genetic FST values generated from reduced-representation bisulfites sequencing (RRBS) read data with a distance value generated from methylation data. The aim here is to compare levels of neutral genomic differentiation to those of methylation differentiation in a specific tissue among closely related but ecologically divergent populations.
I know of several programs that will generate SNPs from bisulfite-converted read data, I am planning to use CGmapTools (Guo et al. 2017). I will then use this SNP data to generate FST values among the populations in question.
I was therefore wondering if anyone had advice about how to generate a comparable FST-equivalent measurement from identified differentially methylated cytosines (DMCs)?