Manipulating base quality scores enables variant calling from bisulfite sequencing alignments using conventional bayesian approaches.

The presented "double-masking" procedure represents an open source, easy-to-use method to facilitate accurate variant calling using conventional software, thus negating any dependency on specialised tools and mitigating the need to generate additional, conventional sequencing libraries alongside bisulfite sequencing experiments. The method is available at https://github.com/bio15anu/revelio and an implementation with Freebayes is available at https://github.com/EpiDiverse/SNP.