BS-SNPer: SNP calling in bisulfite-seq data

作者：Gao, Shengjie; Zou, Dan; Mao, Likai; Liu, Huayu; Song, Pengfei; Chen, Youguo; Zhao, Shancen; Gao, Changduo; Li, Xiangchun; Gao, Zhibo; Fang, Xiaodong; Yang, Huanming; Orntoft, Torben F.^*; Sorensen, Karina D.; Bolund, Lars

来源：Bioinformatics, 2015, 31(24): 4006-4008.

DOI：10.1093/bioinformatics/btv507

• DNA METHYLATION

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.

• 出版日期2015-12-15
• 单位青岛大学; 中国人民解放军国防科学技术大学; 宿州学院; 苏州大学