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 [suYeon|citation]. The

ML estimator with known minor

ML estimator with unknown minor

Estimator from genotype probabilities

Estimator from sequencing data