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.
SFS Estimation
realSFS
This method will estimate the site frequency spectrum, the method is described in Nielsen2012.
This is a 2 step procedure first generate a ".sfs" file, followed by an optimization of the .sfs file which will estimate the Site frequency spectrum. For the optimization we have implemented 2 different approaches both found in the misc subdir of the root subdir
<classdiagram type="dir:LR">
[sequence data]->GL[genotype likelihoods|SAMtools;GATK;SOAPsnp;Kim et.al]
[genotype likelihoods|SAMtools;GATK;SOAPsnp;Kim et.al]->realSFS[.sfs file] [.sfs file]->optimize[.ml file]
</classdiagram>
- -realSFS 1
- an sfs file will be generated.
- -realSFS 2
- snpcalling (not implemented, in this angsd)
- -realSFS 4
- genotypecalling (not implemented, int this angsd)