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Open Access Highly Accessed Method

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

Additional files

Additional file 1:

Detecting heterozygous C/T single nucleotide polymorphisms from Bisulfite-seq data. Hypothetical bisulfite-seq data with all labels as in Figure 1. This illustrates detection of a C/T heterozygous position (left), and that the G-strand alleles can be used to associate methylation state of an adjacent cytosine on the opposite strand with two parental alleles.

Format: PDF Size: 52KB Download file

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Open Data

Additional file 2:

Bis-SNP error frequencies at C:T heterozygous SNPs. The data for heterozygous SNP calling in Figure 3c is broken up into C:T SNPs vs. other heterozygous SNPs.

Format: PDF Size: 156KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Bis-SNP executable, utility scripts, and User Manual. We suggest that the user download the most recent version of these files directly from [37].

Format: GZ Size: 16.6MB Download file

Open Data

Additional file 4:

Bis-SNP source code. We suggest that the user download the most recent version of these files directly from [37].

Format: GZ Size: 114KB Download file

Open Data