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

TY - JOUR

T1 - SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data

AU - Nielsen, Rasmus

AU - Korneliussen, Thorfinn Sand

AU - Albrechtsen, Anders

AU - Li, Yingrui

AU - Wang, Jun

N1 - e37558

PY - 2012/7/24

Y1 - 2012/7/24

N2 - 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.

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.

U2 - 10.1371/journal.pone.0037558

DO - 10.1371/journal.pone.0037558

M3 - Journal article

C2 - 22911679

SN - 1932-6203

VL - 7

JO - PLoS ONE

JF - PLoS ONE

IS - 7

M1 - e37558

ER -