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

Nielsen, Rasmus, Korneliussen, Thorfinn, Albrechtsen, Anders, Li, Yingrui and Wang, Jun (2012) SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data. PLoS ONE, 7 7: . doi:10.1371/journal.pone.0037558


Author Nielsen, Rasmus
Korneliussen, Thorfinn
Albrechtsen, Anders
Li, Yingrui
Wang, Jun
Title SNP calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data
Journal name PLoS ONE   Check publisher's open access policy
ISSN 1932-6203
Publication date 2012-07-24
Sub-type Article (original research)
DOI 10.1371/journal.pone.0037558
Open Access Status DOI
Volume 7
Issue 7
Total pages 11
Place of publication San Francisco, United States
Publisher Public Library of Science
Language eng
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.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Institute for Molecular Bioscience - Publications
 
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