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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## 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 | ||
## here we don't provide prior files, so we directly provide posterior probabilities (ANGSD+sfstools), and therefore we do not correct | ## here we don't provide prior files, so we directly provide posterior probabilities (ANGSD+sfstools), and therefore we do not correct | ||
Revision as of 12:55, 25 June 2013
Matteo Fumagalli has been working on methods to estimate Fst and doing PCA based on ANGSD output files.
Fst
- Generate .sfs files from each population using ANGSD RealSFS
- 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
- here we don't provide prior files, so we directly provide posterior probabilities (ANGSD+sfstools), and therefore we do not correct