title: A fast and accurate SNP detection algorithm for next-generation sequencing data.
abstract: Various methods have been developed for calling single-nucleotide polymorphisms from next-generation sequencing data. However, for satisfactory performance, most of these methods require expensive high-depth sequencing. Here, we propose a fast and accurate single-nucleotide polymorphism detection program that uses a binomial distribution-based algorithm and a mutation probability. We extensively assess this program on normal and cancer next-generation sequencing data from The Cancer Genome Atlas project and pooled data from the 1,000 Genomes Project. We also compare the performance of several state-of-the-art programs for single-nucleotide polymorphism calling and evaluate their pros and cons. We demonstrate that our program is a fast and highly accurate single-nucleotide polymorphism detection method, particularly when the sequence depth is low. The program can finish single-nucleotide polymorphism calling within four hours for 10-fold human genome next-generation sequencing data (30 gigabases) on a standard desktop computer.
authors.affiliation: Department of Biochemistry, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
authors.forename: Feng
authors.initials: F
authors.lastname: Xu
authors.forename: Weixin
authors.initials: W
authors.lastname: Wang
authors.forename: Panwen
authors.initials: P
authors.lastname: Wang
authors.forename: Mulin
authors.initials: M
authors.lastname: Jun Li
authors.forename: Pak
authors.initials: P
authors.lastname: Chung Sham
authors.forename: Junwen
authors.initials: J
authors.lastname: Wang
mesh_terms: D000465:Algorithms; D002891:Chromosomes, Human, Pair 21 / Q000235:genetics; D002892:Chromosomes, Human, Pair 22 / Q000235:genetics; D016678:Genome / Q000235:genetics; D023281:Genomics / Q000379:methods; D005838:Genotype; D006801:Humans; D009369:Neoplasms / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods* / Q000592:standards; D013997:Time Factors