Best practices for SNV and methylation calling from bisulfite sequencing data

The advent of high-throughput sequencing techniques, together withbisulfite treatment of the DNA, allows for genome methylation profiling at asingle cytosine resolution. Some modern tools, as MethylExtract [1], are alsoable to detect variation (SNVs) using the same bisulfite sequencing library,which is crucial for many downstream analyses, for example when decipheringthe impact of sequence variation on differential methylation. However, manyerror sources do exist like sequencing errors, bisulfite failures, clonal reads andsingle nucleotide variants. We evaluate here the impact of all these potential er-ror sources, and provide a list of best practices to overcome them. References1. Barturen, G. Rueda, A. Oliver, J.L. and Hackenberg, M. MethylExtract: High-Quality meth-ylation maps and SNV calling from whole genome bisulfite sequencing data (submitted). IWBBIO 2013. ProceedingsGranada, 18-20 March, 2013125