ANGSD: Analysis of next generation Sequencing Data
Latest tar.gz version is (0.938/0.939 on github), see Change_log for changes, and download it here.
Fst PCA
Matteo Fumagalli has been working on methods to estimate Fst and doing PCA/Covariance based on ANGSD output files.
The main documentation for this is found here: https://github.com/mfumagalli/ngsTools
Fst
- Generate .saf files from each population using ANGSD SFS Estimation
- using a 2D-SFS as a prior, estimated using ngs2dSFS
- using marginal spectra as priors, estimated using emOptim2
PCA
More information here: https://github.com/mfumagalli/ngsTools#ngscovar