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

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

doi:10.1186/gb-2012-13-7-r61

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 journal › Article › peer-review

197 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 language	English
Article number	R61
Journal	Genome Biology
Volume	13
Issue number	7
DOIs	https://doi.org/10.1186/gb-2012-13-7-r61
State	Published - 11 Jul 2012
Externally published	Yes

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].

Access to Document

10.1186/gb-2012-13-7-r61

Cite this

@article{2e5e9d4b79ca447880f013ed71dc2a28,

title = "Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data",

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.",

author = "Yaping Liu and Siegmund, {Kimberly D.} and Laird, {Peter W.} and Berman, {Benjamin P.}",

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].",

year = "2012",

month = jul,

day = "11",

doi = "10.1186/gb-2012-13-7-r61",

language = "אנגלית",

volume = "13",

journal = "Genome Biology",

issn = "1474-7596",

publisher = "BioMed Central Ltd.",

number = "7",

}

TY - JOUR

T1 - Bis-SNP

T2 - Combined DNA methylation and SNP calling for Bisulfite-seq data

AU - Liu, Yaping

AU - Siegmund, Kimberly D.

AU - Laird, Peter W.

AU - Berman, Benjamin P.

N1 - 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].

PY - 2012/7/11

Y1 - 2012/7/11

N2 - 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.

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.

UR - http://www.scopus.com/inward/record.url?scp=84863565553&partnerID=8YFLogxK

U2 - 10.1186/gb-2012-13-7-r61

DO - 10.1186/gb-2012-13-7-r61

M3 - ???researchoutput.researchoutputtypes.contributiontojournal.article???

C2 - 22784381

AN - SCOPUS:84863565553

SN - 1474-7596

VL - 13

JO - Genome Biology

JF - Genome Biology

IS - 7

M1 - R61

ER -

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

Abstract

Bibliographical note

Access to Document

Other files and links

Fingerprint

Cite this