bsgenova: an accurate, robust, and fast genotype caller for bisulfite-sequencing data

文献类型： 外文期刊

第一作者： Feng, Yance

作者： Feng, Yance;Gao, Fei;Gao, Fei

作者机构：

关键词： Genotype; SNP; BS-seq; Bisulfite-sequencing; DNA methylation

期刊名称：BMC BIOINFORMATICS （ 影响因子：3.0； 五年影响因子：4.3 ）

ISSN： 1471-2105

年卷期： 2024 年 25 卷 1 期

页码：

收录情况： SCI

摘要： Background Bisulfite sequencing (BS-Seq) is a fundamental technique for characterizing DNA methylation profiles. Genotype calling from bisulfite-converted BS-Seq data allows allele-specific methylation analysis and the concurrent exploration of genetic and epigenetic profiles. Despite various methods have been proposed, single nucleotide polymorphisms (SNPs) calling from BS-Seq data, particularly for SNPs on chromosome X and in the presence of contaminative data, poses ongoing challenges.Results We introduce bsgenova, a novel SNP caller tailored for bisulfite sequencing data, employing a Bayesian multinomial model. The performance of bsgenova is assessed by comparing SNPs called from real-world BS-Seq data with those from corresponding whole-genome sequencing (WGS) data across three human cell lines. bsgenova is both sensitive and precise, especially for chromosome X, compared with three existing methods. Moreover, in the presence of low-quality reads, bsgenova outperforms other methods notably. In addition, bsgenova is meticulously implemented, leveraging matrix imputation and multi-process parallelization. Compared to existing methods, bsgenova stands out for its speed and efficiency in memory and disk usage. Furthermore, bsgenova integrates bsextractor, a methylation extractor, enhancing its flexibility and expanding its utility.Conclusions We introduce bsgenova for SNP calling from bisulfite-sequencing data. The source code is available at https://github.com/hippo-yf/bsgenova under license GPL-3.0.

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