Inferring Population Structure and Admixture Proportions in Low-Depth NGS Data

. 2018 Aug 21;210(2):719–731. doi: 10.1534/genetics.118.301336

Algorithm 2: Iterative estimation of individual allele frequencies.

1. Estimate population allele frequencies

\hat{p}

from genotype likelihoods (see supplemental material).

2. Estimate posterior genotype probabilities and genotype dosages

E

based on genotype likelihoods and

\hat{p}

3. Estimate

\hat{Π}

using the SVD based method on

E

as described in Algorithm 1.

4. Estimate posterior genotype probabilities and genotype dosages

E

using updated prior information,

\hat{Π} .

5. Repeat steps 3 and 4 until individual allele frequencies have converged.