User:Hussein Alasadi/Notebook/stephens/2013/10/16

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Owwnotebook icon.png Analyzing pooled sequenced data with selection Report.pngMain project page
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Simulating evolution and then pooled sequencing

  • We start with a population of N individuals with a SNP distribution [math] P(M)[/math] ~ [math] N(\mu, \Sigma) [/math].

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 [math] Pois(\lambda) [/math] where [math] \lambda \approx 40-50 [/math]

(2) [math] f_i [/math] (frequency of the ith SNP) ~ [math] B(n, f_i^{true}) [/math]