TY - JOUR AU - Liu, Yaping AU - Siegmund, Kimberly D. AU - Laird, Peter W. AU - Berman, Benjamin P. PY - 2012 DA - 2012/07/11 TI - Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data JO - Genome Biology SP - R61 VL - 13 IS - 7 AB - Bisulfite treatment of DNA followed by high-throughput sequencing (Bisulfite-seq) is an important method for studying DNA methylation and epigenetic gene regulation, yet current software tools do not adequately address single nucleotide polymorphisms (SNPs). Identifying SNPs is important for accurate quantification of methylation levels and for identification of allele-specific epigenetic events such as imprinting. We have developed a model-based bisulfite SNP caller, Bis-SNP, that results in substantially better SNP calls than existing methods, thereby improving methylation estimates. At an average 30× genomic coverage, Bis-SNP correctly identified 96% of SNPs using the default high-stringency settings. The open-source package is available at http://epigenome.usc.edu/publicationdata/bissnp2011. SN - 1474-760X UR - https://doi.org/10.1186/gb-2012-13-7-r61 DO - 10.1186/gb-2012-13-7-r61 ID - Liu2012 ER -