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

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Analyzing pooled sequenced data with selection Main project page
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Simulating evolution and then pooled sequencing

  • We start with a population of N individuals with a certain SNP distribution P(M) ~ N(μ,Σ).

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 Pois(λ) where  \lambda \approx 40-50

(2) fi (frequency of the ith SNP) ~  B(n, f_i^{true})

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