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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;THIS PAGE IS OBSOLETE, PLEASE SEE FST AND PCA in the sidebar for the latest versions | |||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. | Matteo Fumagalli has been working on methods to estimate Fst and doing PCA/Covariance based on ANGSD output files. | ||
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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= | ||
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- THIS PAGE IS OBSOLETE, PLEASE SEE FST AND PCA in the sidebar for the latest versions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
- 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