2d SFS Estimation

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.

And is best explained by a full example.

Example

• Assume you have a 12 bamfiles for population in the file pop1.list'
• Assume you have a 14 bamfiles for population in the file pop2.list
• Assume you have a fastafile containing the ancestral state in the and.fa