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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data. / Nielsen, Rasmus; Korneliussen, Thorfinn Sand; Albrechtsen, Anders; Li, Yingrui; Wang, Jun.

In: PLoS ONE, Vol. 7, No. 7, e37558, 2012.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Nielsen, R, Korneliussen, TS, Albrechtsen, A, Li, Y & Wang, J 2012, 'SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data', PLoS ONE, vol. 7, no. 7, e37558. https://doi.org/10.1371/journal.pone.0037558

APA

Nielsen, R., Korneliussen, T. S., Albrechtsen, A., Li, Y., & Wang, J. (2012). SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data. PLoS ONE, 7(7), [e37558]. https://doi.org/10.1371/journal.pone.0037558

Vancouver

Nielsen R, Korneliussen TS, Albrechtsen A, Li Y, Wang J. SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data. PLoS ONE. 2012;7(7). e37558. https://doi.org/10.1371/journal.pone.0037558

Author

Nielsen, Rasmus ; Korneliussen, Thorfinn Sand ; Albrechtsen, Anders ; Li, Yingrui ; Wang, Jun. / SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data. In: PLoS ONE. 2012 ; Vol. 7, No. 7.

Bibtex

@article{9115b976bf424b1f9a1de08605d7fcbd,
title = "SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data",
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.",
author = "Rasmus Nielsen and Korneliussen, {Thorfinn Sand} and Anders Albrechtsen and Yingrui Li and Jun Wang",
note = "e37558",
year = "2012",
doi = "10.1371/journal.pone.0037558",
language = "English",
volume = "7",
journal = "PLoS ONE",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "7",

}

RIS

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

Y1 - 2012

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

VL - 7

JO - PLoS ONE

JF - PLoS ONE

SN - 1932-6203

IS - 7

M1 - e37558

ER -

ID: 44047265