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 SNP distribution P(M) ~ N(μ,Σ).

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 Pois(λ) where  \lambda \approx 40-50

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

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