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SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data

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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 how the method can be used for genotype calling and SNP calling. We also show how the method can be extended to various other cases including cases with deviations from Hardy-Weinberg equilibrium. We evaluate the statistical properties of the methods using simulations and by application to a real data set.
Original languageEnglish
Article numbere37558
JournalPLoS ONE
Volume7
Issue number7
Number of pages11
ISSN1932-6203
DOIs
Publication statusPublished - 2012

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