pWGBSSimla: a profile-based whole-genome bisulphite sequencing data simulator incorporating methylation QTLs, allele-specific methylations and differentially methylated regions

Motivation DNA methylation plays an important role in regulating gene expression. There has been growing interest in investigating the roles that genetic variants play in changing the methylation levels (i.e., methylation quantitative trait loci or meQTLs), how methylation regulates the imprinting of gene expression (i.e., allele-specific methylation or ASM), and the differentially methylated regions (DMRs) among different cell types. However, none of the current simulation tools can generate whole-genome bisulphite sequencing (WGBS) data while modeling meQTLs, ASM, and DMRs. Results We developed pWGBSSimla, a profile-based WGBS data simulator, which simulates WGBS data for 29 cell types based on real data. meQTLs and ASM are modeled based on the block structures of methylation status at CpGs, and DMRs are simulated based on observations of methylation rates in real data. Availability pWGBSSimla is available at http://omicssimla.sourceforge.io .