PCA

Genotype likelihood approach

Matteo Fumagallis methods for doing PCA/Covariance based on ANGSD output files:

Fumagalli, M, Vieira, FG, Korneliussen, TS, Linderoth, T, Huerta-Sánchez, E, Albrechtsen, A, Nielsen, R (2013). Quantifying population genetic differentiation from next-generation sequencing data. Genetics, 195, 3:979-92.

This works without the need to call SNPs or genotypes based on genotype likelihoods

The main documentation for this is found here: https://github.com/mfumagalli/ngsTools and here https://github.com/mfumagalli/ngsTools#ngscovar

single read sampling

Both PCA and MDS can be performed based on sampling of a single read at each site. This can work even with very low depth data e.g. <1X. This method can be PCA_MDS found here. However, it requires low error rate and polymorphic sites need to be inferred (or provided by user)