SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data.
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ABSTRACT:
SUBMITTER: Nielsen R
PROVIDER: S-EPMC3404070 | biostudies-literature | 2012
REPOSITORIES: biostudies-literature
Publications
SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data.
Nielsen Rasmus R Korneliussen Thorfinn T Albrechtsen Anders A Li Yingrui Y Wang Jun J Wang Jun J
PloS one 20120724 7
We present a statistical framework for estimation and application of sample allele frequency spectra from New-Generation Sequencing (NGS) data. In this method, we first estimate the allele frequency spectrum using maximum likelihood. In contrast to previous methods, the likelihood function is calculated using a dynamic programming algorithm and numerically optimized using analytical derivatives. We then use a bayesian method for estimating the sample allele frequency in a single site, and show h ...[more]
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