ANGSD: Analysis of next generation Sequencing Data

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Fst PCA

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THIS PAGE IS OBSOLETE, PLEASE SEE FST AND PCA in the sidebar for the latest versions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: https://github.com/mfumagalli/ngsTools

Fst

  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

PCA

More information here: https://github.com/mfumagalli/ngsTools#ngscovar

cite

If you use these methods, you should cite the m. fumagalli paper http://www.ncbi.nlm.nih.gov/pubmed/23979584