ANGSD: Analysis of next generation Sequencing Data
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SFS Estimation: Difference between revisions
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This is a 2 step procedure first generate a ".sfs" file using -realSFS 1. And then do an optimization of the .sfs file which will estimate the Site frequency spectrum. | This is a 2 step procedure first generate a ".sfs" file using -realSFS 1. And then do an optimization of the .sfs file which will estimate the Site frequency spectrum. | ||
<classdiagram> | <classdiagram type="dir:LR"> | ||
[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] | ||
Revision as of 15:08, 10 October 2012
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 using -realSFS 1. And then do an optimization of the .sfs file which will estimate the Site frequency spectrum.
<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)