The study of epigenetic heterogeneity at the level of individual cells and in 
whole populations is the key to understanding cellular differentiation, 
organismal development, and the evolution of cancer. We develop a statistical 
method, epiG, to infer and differentiate between different epi-allelic 
haplotypes, annotated with CpG methylation status and DNA polymorphisms, from 
whole-genome bisulfite sequencing data, and nucleosome occupancy from NOMe-seq 
data. We demonstrate the capabilities of the method by inferring allele-specific 
methylation and nucleosome occupancy in cell lines, and colon and tumor samples, 
and by benchmarking the method against independent experimental data.