Albrecht at 15:12, 26 February 2014

2014-02-26T15:12:53Z

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	~~==Method 1==~~

	The method is described in [[kim2011]] and work by simultaneously estimating allele frequencies, genotype likelihoods and the error rates.		The method is described in [[kim2011]] and work by simultaneously estimating allele frequencies, genotype likelihoods and the error rates.

Albrecht: Created page with "==Method 1== The method is described in kim2011 and work by simultaneously estimating allele frequencies, genotype likelihoods and the error rates. The likelihood of t..."

2014-02-26T15:12:40Z

Created page with "==Method 1== The method is described in kim2011 and work by simultaneously estimating allele frequencies, genotype likelihoods and the error rates. The likelihood of t..."

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==Method 1==

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

<math> \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}</math>

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

<math> \hat{e},\hat{f} = argmax_{f,e} p(D|f,e)</math>

ErrorSykMethod - Revision history

Albrecht at 15:12, 26 February 2014

Albrecht: Created page with "==Method 1== The method is described in kim2011 and work by simultaneously estimating allele frequencies, genotype likelihoods and the error rates. The likelihood of t..."