title: BS-SNPer: SNP calling in bisulfite-seq data.
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.
  
  
  METHODS
  BS-SNPer is written in C++ and Perl, and is freely available at https://github.com/hellbelly/BS-Snper.
authors: Department of Biomedicine, Aarhus University, Aarhus, Denmark, BGI Co. Ltd., Shenzhen 518083, China, BioInformatics Research Center (BIRC), Aarhus University, Aarhus 8000, Denmark.
authors: Shengjie
authors: S
authors: Gao
authors: BGI Co. Ltd., Shenzhen 518083, China, School of Computer, National University of Defense Technology, Changsha 410073, China.
authors: Dan
authors: D
authors: Zou
authors: BGI Co. Ltd., Shenzhen 518083, China, Genomic Biology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia.
authors: Likai
authors: L
authors: Mao
authors: Departments of Biostatistics and Informatics, University of Colorado-Anschutz Medical Campus, Denver 80204, USA.
authors: Huayu
authors: H
authors: Liu
authors: The Fourth People's Hospital of Shenzhen (Futian hospital), Shenzhen, 518033, China.
authors: Pengfei
authors: P
authors: Song
authors: Department of Obsterics and Gynecology,the First Hospital Affiliated to Suzhou University, Jiangsu Suzhou 215006,China.
authors: Youguo
authors: Y
authors: Chen
authors: BGI Co. Ltd., Shenzhen 518083, China.
authors: Shancen
authors: S
authors: Zhao
authors: College of Information Engineering, Qingdao University, Qingdao 266071, China and.
authors: Changduo
authors: C
authors: Gao
authors: BGI Co. Ltd., Shenzhen 518083, China.
authors: Xiangchun
authors: X
authors: Li
authors: BGI Co. Ltd., Shenzhen 518083, China.
authors: Zhibo
authors: Z
authors: Gao
authors: BGI Co. Ltd., Shenzhen 518083, China.
authors: Xiaodong
authors: X
authors: Fang
authors: BGI Co. Ltd., Shenzhen 518083, China.
authors: Huanming
authors: H
authors: Yang
authors: Department of Molecular Medicine, Aarhus University Hospital, Aarhus 8000, Denmark.
authors: Torben F
authors: TF
authors: Ørntoft
authors: Department of Molecular Medicine, Aarhus University Hospital, Aarhus 8000, Denmark.
authors: Karina D
authors: KD
authors: Sørensen
authors: Department of Biomedicine, Aarhus University, Aarhus, Denmark, BGI Co. Ltd., Shenzhen 518083, China, BioInformatics Research Center (BIRC), Aarhus University, Aarhus 8000, Denmark.
authors: Lars
authors: L
authors: Bolund
mesh_terms: D000483:Alleles; D019175:DNA Methylation; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013447:Sulfites
chemical_list: D013447:Sulfites; C009279:sodium bisulfite