Latest revision as of 15:21, 30 July 2015

THIS PAGE IS OBSOLETE, PLEASE SEE FST AND PCA in the sidebar for the latest versions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

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

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

@@ Line 1: / Line 1: @@
-Matteo Fumagalli has been working on methods to estimate Fst and doing PCA based on ANGSD output files.
+;THIS PAGE IS OBSOLETE, PLEASE SEE FST AND PCA in the sidebar for the latest versions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=
-# Generate .sfs files from each population using ANGSD [[RealSFS]]
+# Generate .saf files from each population using ANGSD [[SFS Estimation]]
-# Estimate the .sfs.ml or .sfs.em.ml for each .sfs file
 ## using a 2D-SFS as a prior, estimated using ngs2dSFS
-## using marginal spectra as priors, estimated using optimSFS
+## using marginal spectra as priors, estimated using '''realSFS'''
-## here we don't provide prior files, so we directly provide posterior probabilities (ANGSD+sfstools), and therefore we do not correct
+=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