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Article

SNP calling, genotype calling, and sample allele frequency estimation from New-Generation Sequencing data.

PloS one - 1 Jan 2012

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

Abstract excerpt

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...

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PMID: 22911679
DOI: 10.1371/journal.pone.0037558
PMCID: PMC3404070

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