SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data

Wei, Zhi, Wang, Wei, Hu, Pingzhao, Lyon, Gholson J., Hakonarson, Hakon (2011) SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data. Nucleic Acids Research, 39 (19). e132. ISSN 03051048 (ISSN)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/21813454
DOI: 10.1093/nar/gkr599

Abstract

We develop a statistical tool SNVer for calling common and rare variants in analysis of pooled or individual next-generation sequencing (NGS) data. We formulate variant calling as a hypothesis testing problem and employ a binomial-binomial model to test the significance of observed allele frequency against sequencing error. SNVer reports one single overall P-value for evaluating the significance of a candidate locus being a variant based on which multiplicity control can be obtained. This is particularly desirable because tens of thousands loci are simultaneously examined in typical NGS experiments. Each user can choose the false-positive error rate threshold he or she considers appropriate, instead of just the dichotomous decisions of whether to 'accept or reject the candidates' provided by most existing methods. We use both simulated data and real data to demonstrate the superior performance of our program in comparison with existing methods. SNVer runs very fast and can complete testing 300 K loci within an hour. This excellent scalability makes it feasible for analysis of whole-exome sequencing data, or even whole-genome sequencing data using high performance computing cluster. SNVer is freely available at http://snver.sourceforge.net/.

Item Type: Paper
Uncontrolled Keywords: Gene Frequency Genetic Variation High-Throughput Nucleotide Sequencing Models, Statistical Polymorphism, Single Nucleotide Software
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > SNP
CSHL Authors:
Communities: CSHL labs > Lyon lab
Depositing User: Matt Covey
Date Deposited: 10 Dec 2012 20:13
Last Modified: 10 Dec 2012 21:18
PMCID: PMC3201884
URI: http://repository.cshl.edu/id/eprint/26302

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