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: Difference between revisions
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# Generate .saf files from each population using ANGSD [[SFS Estimation]] | # Generate .saf files from each population using ANGSD [[SFS Estimation]] | ||
## using a 2D-SFS as a prior, estimated using ngs2dSFS | ## using a 2D-SFS as a prior, estimated using ngs2dSFS | ||
## using marginal spectra as priors, estimated using | ## using marginal spectra as priors, estimated using '''realSFS''' | ||
=PCA= | =PCA= | ||
Revision as of 12:23, 30 June 2014
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 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