Abstract
Bisulfite sequencing (BS-seq) remains the gold standard technique to detect DNA methylation profiles at single-nucleotide resolution. The DNA methylation status of CpG sites on the same fragment represents a discrete methylation haplotype (mHap). The mHap-level metrics were demonstrated to be promising cancer biomarkers and explain more gene expression variation than average methylation. However, most existing tools focus on average methylation and ne-glect mHap patterns. Here, we present mhapTk, a comprehensive toolkit for analysis of DNA methylation haplotypes. It calculates eight mHap-level summary statistics in predefined regions or across individual CpG in a genome-wide manner. It identifies methylation haplotype blocks (MHBs), in which methylation of pairwise CpGs are tightly correlated. Furthermore, mHap pat-terns can be visualized with the built-in functions in mHapTk or external tools such as IGV and deepTools.
