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 [math]\displaystyle{ P(M) }[/math] ~ [math]\displaystyle{ N(\mu, \Sigma) }[/math].

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

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





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