ANGSD: Analysis of next generation Sequencing Data
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ErrorSykMethod
From angsd
The method is described in kim2011 and work by simultaneously estimating allele frequencies, genotype likelihoods and the error rates.
The likelihood of the sequencing data of
individuals for
sites can be described through the allele frequencies
and the type specific error rates
by summing over the unknown genotypes . The genotype likelihood
relies on the type specific error rates (see kim2011 p.14 for details). The type specific error rates are obtain along site the allele frequencies by