BS-SNPer: SNP calling in bisulfite-seq data

Shengjie Gao; Dan Zou; Likai Mao; Huayu Liu; Pengfei Song; Youguo Chen; Shancen Zhao; Changduo Gao; Xiangchun Li; Zhibo Gao; Xiaodong Fang; Huanming Yang; Torben F Ørntoft; Karina D Sørensen; Lars Bolund

doi:10.1093/bioinformatics/btv507

BS-SNPer: SNP calling in bisulfite-seq data

Bioinformatics. 2015 Dec 15;31(24):4006-8. doi: 10.1093/bioinformatics/btv507. Epub 2015 Aug 28.

Authors

Shengjie Gao¹, Dan Zou², Likai Mao³, Huayu Liu⁴, Pengfei Song⁵, Youguo Chen⁶, Shancen Zhao⁷, Changduo Gao⁸, Xiangchun Li⁷, Zhibo Gao⁷, Xiaodong Fang⁷, Huanming Yang⁷, Torben F Ørntoft⁹, Karina D Sørensen⁹, Lars Bolund¹

Affiliations

¹ Department of Biomedicine, Aarhus University, Aarhus, Denmark, BGI Co. Ltd., Shenzhen 518083, China, BioInformatics Research Center (BIRC), Aarhus University, Aarhus 8000, Denmark.
² BGI Co. Ltd., Shenzhen 518083, China, School of Computer, National University of Defense Technology, Changsha 410073, China.
³ BGI Co. Ltd., Shenzhen 518083, China, Genomic Biology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
⁴ Departments of Biostatistics and Informatics, University of Colorado-Anschutz Medical Campus, Denver 80204, USA.
⁵ The Fourth People's Hospital of Shenzhen (Futian hospital), Shenzhen, 518033, China.
⁶ Department of Obsterics and Gynecology,the First Hospital Affiliated to Suzhou University, Jiangsu Suzhou 215006,China.
⁷ BGI Co. Ltd., Shenzhen 518083, China.
⁸ College of Information Engineering, Qingdao University, Qingdao 266071, China and.
⁹ Department of Molecular Medicine, Aarhus University Hospital, Aarhus 8000, Denmark.

Abstract

Sodium bisulfite conversion followed by sequencing (BS-Seq, such as whole genome bisulfite sequencing or reduced representation bisulfite sequencing) has become popular for studying human epigenetic profiles. Identifying single nucleotide polymorphisms (SNPs) is important for quantification of methylation levels and for study of allele-specific epigenetic events such as imprinting. However, SNP calling in such data is complex and time consuming. Here, we present an ultrafast and memory-efficient package named BS-SNPer for the exploration of SNP sites from BS-Seq data. Compared with Bis-SNP, a popular BS-Seq specific SNP caller, BS-SNPer is over 100 times faster and uses less memory. BS-SNPer also offers higher sensitivity and specificity compared with existing methods.

Availability and implementation: BS-SNPer is written in C++ and Perl, and is freely available at https://github.com/hellbelly/BS-Snper.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alleles
DNA Methylation*
Humans
Polymorphism, Single Nucleotide*
Sequence Analysis, DNA / methods*
Software*
Sulfites*

Substances

Sulfites
sodium bisulfite