BS-SNPer

BS-SNPer detects single nucleotide polymorphisms (SNPs) from bisulfite sequencing (BS-Seq) data to support analysis of DNA methylation and allele-specific epigenetic events such as imprinting.

Key Features:

• Performance Efficiency: Is over 100 times faster than Bis-SNP while using less memory, facilitating high-throughput SNP calling on BS-Seq datasets.
• Sensitivity and Specificity: Provides higher sensitivity and specificity in SNP detection compared to existing BS-Seq specific methods.
• Implementation: Implemented in C++ and Perl.
• Bayesian Modeling and Input Formats: Uses approximate Bayesian modeling to evaluate SNP sites from alignments in standard BAM/SAM format.

Scientific Applications:

• SNP calling in BS-Seq experiments: Detects SNPs in whole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) datasets.
• Epigenetic and allele-specific analyses: Enables joint analysis of genetic variation and DNA methylation, including allele-specific methylation and imprinting studies.

Methodology:

Applies approximate Bayesian modeling to call SNPs from alignments provided in BAM/SAM format.