< User:Hussein Alasadi‎ | Notebook‎ | stephens‎ | 2013‎ | 10
Analyzing pooled sequenced data with selection <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
<html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</html>

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