SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data
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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.
I: PLoS ONE, Bind 7, Nr. 7, e37558, 2012.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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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