MethHaplo: Combining Allele-specific DNA Methylation and SNPs for Haplotype Region Identification, click here for information on how to use it and source code.
DNA methylation is an important epigenetic modification that plays a critical role in most eukaryotic organisms. Parental alleles in haploid genomes may exhibit different methylation patterns, which can lead to different phenotypes and even different therapeutic and drug responses to diseases. We developed a new method, MethHaplo, that identify DNA methylation haplotype regions with allele-specific DNA methylation and single nucleotide polymorphisms (SNPs) from whole-genome bisulfite sequencing (WGBS) data. When we integrate WGBS and high-throughput chromosome conformation capture (Hi-C) data, MethHaplo could call even longer haplotypes. By constructing methylation haplotypes for various cell lines, we provide a clearer picture of the effect of DNA methylation on gene expression, histone modification and three-dimensional chromosome structure at the haplotype level. Our method could benefit the study of parental inheritance-related disease and heterosis in agriculture.