< 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
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## Simulating evolution and then pooled sequencing

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

We can use Dick Hudson's MsSel (MS with selection) to generate a SNP distribution.

• We then evolve the populations for g generations with selection for SNP j

In MsSel, we can specify an allele frequency trajectory for a site. We can generate a trajectory based on a simple W-F simulation with selection.

Or, we may have to use forqs.

• 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) ~ $\displaystyle B(n, f_i^{true})$