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. Also Forqs was written in way with selection experiments in mind, they have functions such as "Quantitative Trait" that allows the user to define the fitness function in a complex way.

  • 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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