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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\u00d7 genomic coverage, Bis-SNP correctly identified 96% of SNPs using the default high-stringency settings. The open-source package is available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/epigenome.usc.edu\/publicationdata\/bissnp2011\">http:\/\/epigenome.usc.edu\/publicationdata\/bissnp2011<\/jats:ext-link>.<\/jats:p>","DOI":"10.1186\/gb-2012-13-7-r61","type":"journal-article","created":{"date-parts":[[2012,7,11]],"date-time":"2012-07-11T16:13:38Z","timestamp":1342023218000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":246,"title":["Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data"],"prefix":"10.1186","volume":"13","author":[{"given":"Yaping","family":"Liu","sequence":"first","affiliation":[]},{"given":"Kimberly D","family":"Siegmund","sequence":"additional","affiliation":[]},{"given":"Peter W","family":"Laird","sequence":"additional","affiliation":[]},{"given":"Benjamin P","family":"Berman","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,7,11]]},"reference":[{"key":"2899_CR1","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1038\/nrg2732","volume":"11","author":"PW Laird","year":"2010","unstructured":"Laird PW: Principles and challenges of genomewide DNA methylation analysis. 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