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

Rasmus Nielsen; Thorfinn Sand Korneliussen; Anders Albrechtsen; Yingrui Li; Jun Wang

doi:10.1371/journal.pone.0037558

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

Rasmus Nielsen, Thorfinn Sand Korneliussen, Anders Albrechtsen, Yingrui Li, Jun Wang

186 Citations (Scopus)

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Abstract

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 language	English
Article number	e37558
Journal	PLoS ONE
Volume	7
Issue number	7
Number of pages	11
ISSN	1932-6203
DOIs	https://doi.org/10.1371/journal.pone.0037558
Publication status	Published - 24 Jul 2012

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Nielsen_2012_SNP_callingFinal published version, 1.25 MBLicence: CC BY

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AU - Korneliussen, Thorfinn Sand

AU - Albrechtsen, Anders

AU - Li, Yingrui

AU - Wang, Jun

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AB - 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.

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

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