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Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

Yaping Liu12, Kimberly D Siegmund3, Peter W Laird1 and Benjamin P Berman13*

Author Affiliations

1 USC Epigenome Center, University of Southern California, 1450 Biggy Street, Los Angeles, CA 90089, USA

2 Genetics, Molecular and Cellular Biology Program, University of Southern California, 1975 Zonal Avenue KAM-B16, Los Angeles, CA 90089, USA

3 Department of Preventive Medicine, Keck School of Medicine, University of Southern California, 1441 Eastlake Avenue, Los Angeles, CA 90089, USA

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Genome Biology 2012, 13:R61  doi:10.1186/gb-2012-13-7-r61

Published: 11 July 2012

Abstract

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 webcite.