# Difference between revisions of "User:Hussein Alasadi/Notebook/stephens/2013/10/16"

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## Simulating evolution and then pooled sequencing

• We start with a population of N individuals with a certain SNP distribution $\displaystyle P(M)$ ~ $\displaystyle N(\mu, \Sigma)$ .

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 (n) from $\displaystyle Pois(\lambda)$ where $\displaystyle \lambda \approx 40-50$

(2) $\displaystyle f_i$ (frequency of the ith SNP) ~ $\displaystyle B(n, f_i^{true})$