ANGSD: Analysis of next generation Sequencing Data

Latest tar.gz version is (0.934/0.935 on github), see Change_log for changes, and download it here.


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Estimator from genotype probabilities

If the genotype probabilities are known the frequencies can be estimated by summing up the posterior probabilities  p(G=g|D) where D is the sequencing data and g\in\{0,1,2\} the allele count of the minor allele. The frequency estimate

  \hat{f}=\frac{1}{2N}\sum_i^N \left(2p(G=2|D)+p(G=1|D)\right)