SNP calling using genotype model selection on high-throughput sequencing data

doi:10.1093/bioinformatics/bts001

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	SNP calling using genotype model selection on high-throughput sequencing data
	You, Na 2; Murillo, Gabriel 1; Su, Xiaoquan3 ; Zeng, Xiaowei 3; Xu, Jian3 ; Ning, Kang 3; Zhang, Shoudong 4; Zhu, Jiankang 4,5; Cui, Xinping 1,6
	2012-03-01
发表期刊	BIOINFORMATICS
卷号	28 期号:5 页码:643-650
摘要	MOTIVATION: A review of the available single nucleotide polymorphism (SNP) calling procedures for Illumina high-throughput sequencing (HTS) platform data reveals that most rely mainly on base-calling and mapping qualities as sources of error when calling SNPs. Thus, errors not involved in base-calling or alignment, such as those in genomic sample preparation, are not accounted for. RESULTS: A novel method of consensus and SNP calling, Genotype Model Selection (GeMS), is given which accounts for the errors that occur during the preparation of the genomic sample. Simulations and real data analyses indicate that GeMS has the best performance balance of sensitivity and positive predictive value among the tested SNP callers. ; Motivation: A review of the available single nucleotide polymorphism (SNP) calling procedures for Illumina high-throughput sequencing (HTS) platform data reveals that most rely mainly on base- calling and mapping qualities as sources of error when calling SNPs. Thus, errors not involved in base- calling or alignment, such as those in genomic sample preparation, are not accounted for.
文章类型	Article
学科领域	功能基因组
WOS标题词	Science & Technology ; Life Sciences & Biomedicine ; Technology ; Physical Sciences
DOI	10.1093/bioinformatics/bts001
关键词[WOS]	DISCOVERY ; FRAMEWORK
收录类别	SCI
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
WOS记录号	WOS:000300986600007
引用统计
文献类型	期刊论文
条目标识符	http://ir.qibebt.ac.cn/handle/337004/1419
专题	单细胞中心组群
作者单位	1.Univ Calif Riverside, Dept Stat, Riverside, CA 92521 USA 2.Sun Yat Sen Univ, Sch Math & Computat Sci, Dept Stat Sci, Guangzhou 510275, Guangdong, Peoples R China 3.Chinese Acad Sci, Qingdao Inst BioEnergy & Bioproc Technol, Qingdao 266101, Peoples R China 4.King Abdullah Univ Sci & Technol, Plant Stress Genom & Technol Res Ctr, Thuwal 239556900, Saudi Arabia 5.Purdue Univ, Dept Hort & Landscape Architecture, W Lafayette, IN 47907 USA 6.Univ Calif Riverside, Inst Integrat Genome Biol, Ctr Plant Cell Biol, Riverside, CA 92521 USA
推荐引用方式 GB/T 7714	You, Na,Murillo, Gabriel,Su, Xiaoquan,et al. SNP calling using genotype model selection on high-throughput sequencing data[J]. BIOINFORMATICS,2012,28(5):643-650.
APA	You, Na.,Murillo, Gabriel.,Su, Xiaoquan.,Zeng, Xiaowei.,Xu, Jian.,...&Cui, Xinping.(2012).SNP calling using genotype model selection on high-throughput sequencing data.BIOINFORMATICS,28(5),643-650.
MLA	You, Na,et al."SNP calling using genotype model selection on high-throughput sequencing data".BIOINFORMATICS 28.5(2012):643-650.

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