SFS Estimation

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.This is shown in the diagram below.

<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[.sfs.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)