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

Yaping Liu, Kimberly D. Siegmund, Peter W. Laird, Benjamin P. Berman*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

192 Scopus citations

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.

Original languageAmerican English
Article numberR61
JournalGenome Biology
Volume13
Issue number7
DOIs
StatePublished - 11 Jul 2012
Externally publishedYes

Bibliographical note

Funding Information:
Support to YL, PWL, and BPB was provided by NIH grant number U24CA143882. We acknowledge our colleagues at the USC Epigenome Center for useful discussions and suggestions. High performance computing support was provided by the USC High Performance Computing Center [45].

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