ErrorSykMethod

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 $D$ of $n$ individuals for $M$ sites can be described through the allele frequencies $f$ and the type specific error rates $e$

$$ \begin{align} p(D|f,e) &= \prod_{i=1}^n \prod_{j=1}^M p(D_j^i|f_j,e)\\ &= \prod_{i=1}^n \prod_{j=1}^M \sum_{g=0}^2 p(g|f_j)p(D_j^i|g,e) \end{align} $$

by summing over the unknown genotypes $g$. The genotype likelihood $p(D_j^i|g,e)$ 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

$$ \hat{e},\hat{f} = argmax_{f,e} p(D|f,e) $$