ANGSD: Analysis of next generation Sequencing Data
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Fst PCA: Difference between revisions
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Matteo Fumagalli has been working on methods to estimate Fst and doing PCA based on ANGSD output files. | 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= | =Fst= | ||
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## 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 optimSFS | ## using marginal spectra as priors, estimated using optimSFS | ||
# | |||
=PCA= | |||
More information here: | |||
https://github.com/mfumagalli/ngsTools#ngscovar | |||
Revision as of 13:03, 25 June 2013
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
- using a 2D-SFS as a prior, estimated using ngs2dSFS
- using marginal spectra as priors, estimated using optimSFS
PCA
More information here: https://github.com/mfumagalli/ngsTools#ngscovar