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: Difference between revisions
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[sequence data]->GL[genotype likelihoods|SAMtools;GATK;SOAPsnp;Kim et.al] | [sequence data]->GL[genotype likelihoods|SAMtools;GATK;SOAPsnp;Kim et.al] | ||
[genotype likelihoods|SAMtools;GATK;SOAPsnp;Kim et.al]->realSFS[.sfs file] | [genotype likelihoods|SAMtools;GATK;SOAPsnp;Kim et.al]->realSFS[.sfs file] | ||
[.sfs file]->optimize[.ml file] | [.sfs file]->optimize[.sfs.ml file] | ||
</classdiagram> | </classdiagram> | ||
Revision as of 15:26, 10 October 2012
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)