ANGSD: Analysis of next generation Sequencing Data

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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 14:26, 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)