BS-SNPer: SNP Calling in Bisulfite-seq Data

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2015 Aug 31

PMID 26319221

Citations 39

Authors

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 Orntoft

Karina D Sorensen

Lars Bolund

Affiliations

Soon will be listed here.

Abstract

Unlabelled: 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.

Citing Articles

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