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

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

SUBMITTER: Wei Z 

PROVIDER: S-EPMC3201884 | biostudies-literature | 2011 Oct

REPOSITORIES: biostudies-literature