ANGSD: Analysis of next generation Sequencing Data

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Allele Frequencies

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Allele Frequency estimation

-doMaf [int]

INT=1 bfgs known minor

INT=2 EM known minor

INT=4 BFGS unknown minor

INT=8 EM unknown minor

INT=16 frequencies from genotype probabilities

Allele frequencies from genotype likelihoods

The allele frequency estimators are described in citation. The

ML estimator with known minor

ML estimator with unknown minor

Estimator from genotype probabilities

Estimator from sequencing data