Fig. 1: Comparison of hap-ASM analysis methods.
From: Detection of haplotype-dependent allele-specific DNA methylation in WGBS data
WGBS reads (rows) corresponding to each homologous allele of a haplotype are used by each method to estimate the probability distribution of methylation (PDM) within each allele. The NPI method provides an empirical estimate of the PDM at each CpG site using WGBS observations of its methylation state (orange rectangles). The NPD method provides an empirical estimate of the joint PDM within an epiallele, composed of a few CpG sites (usually 4) around an SNP, using only full WGBS observations of its methylation state (yellow rectangles). The CPEL method performs haplotype-dependent allele-specific methylation analysis by estimating the joint PDM at all CpG sites within a homologous allele using the entire set of WGBS data (blue rectangles), thus utilizing all available methylation information and allowing modeling of the cooperative effect of multiple SNPs on DNA methylation.
