ANGSD: Analysis of next generation Sequencing Data
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Fst PCA: Difference between revisions
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(Created page with "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...") |
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=Fst= | =Fst= | ||
# Generate .sfs files from each population using ANGSD [[RealSFS]] | # 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 | |||
## | |||
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