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.
RealSFS
This program will estimate the SFS based on a .saf file generated from the ./angsd [options] -doSaf .
Brief overview
./emOptim2 afile.saf nChr [-start FNAME -P nThreads -tole tole -maxIter -nSites ] nChr is the number of chromosomes. (twice the number of diploid invididuals)
Program defaults to use the EM algorithm for the optimisation, the BFGS method can used by supplying BFGS as the first argument after ./emOptim2
Output
Main results are printed to the stdout. Values are in logspace.
NB
Use as many sites as possible, for more reliable estimates.