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.


From angsd
Jump to navigation Jump to search
THIS PAGE IS OBSOLETE, PLEASE SEE FST AND PCA in the sidebar for the latest versions

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:


  1. Generate .saf files from each population using ANGSD SFS Estimation
    1. using a 2D-SFS as a prior, estimated using ngs2dSFS
    2. using marginal spectra as priors, estimated using realSFS


More information here:


If you use these methods, you should cite the m. fumagalli paper