ANGSD: Analysis of next generation Sequencing Data
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SFS Estimation: Difference between revisions
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This method will estimate the site frequency spectrum, the method is described in [[Nielsen2012]]. | 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 | 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"> | <classdiagram type="dir:LR"> | ||
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;-realSFS 1: | ;-realSFS 1: an sfs file will be generated. | ||
;-realSFS 2: snpcalling (not implemented, in this angsd) | ;-realSFS 2: snpcalling (not implemented, in this angsd) | ||
;-realSFS 4: genotypecalling (not implemented, int this angsd) | ;-realSFS 4: genotypecalling (not implemented, int this angsd) | ||
Revision as of 14:18, 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, 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)