ANGSD: Analysis of next generation Sequencing Data
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2d SFS Estimation: Difference between revisions
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Angsd can estimate a 2d site frequency spectrum. This is an extension of the 1d site frequency spectrum [[SFS Estimation|method]]. | Angsd can estimate a 2d site frequency spectrum. This is an extension of the 1d site frequency spectrum [[SFS Estimation|method]]. | ||
The method works by calculating population specific sample allele frequencies. A minor annoyance in the current implementation is that you will need to limit the analysis to the sites that has coverage in both population. This in effect means that you will need to do two passes for each population. | |||
=Example= | |||
Revision as of 22:30, 12 March 2014
Angsd can estimate a 2d site frequency spectrum. This is an extension of the 1d site frequency spectrum method.
The method works by calculating population specific sample allele frequencies. A minor annoyance in the current implementation is that you will need to limit the analysis to the sites that has coverage in both population. This in effect means that you will need to do two passes for each population.