Analyzing pooled sequenced data with selection Main project page
Previous entry

Simulating evolution and then pooled sequencing

• We start with a population of N individuals with a certain SNP distribution P(M) ~ N(μ,Σ).

To do this we can use Dick Hudson's MS to lay down neutral variants (but the distribution really does not matter).

• We then evolve the populations for g generations with recombination

To do this we can use Kessner's Forqs. Forqs allows the user to specify the recombination rate file which might be useful in the future.

• Simulate pooled sequencing

(1) draw a coverage from Pois(λ) where $\lambda \approx 40-50$