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

Analyzing pooled sequenced data with selection

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Simulating evolution and then pooled sequencing We start with a population of N individuals with a SNP distribution [math]\displaystyle{ P(M) }[/math] ~ [math]\displaystyle{ 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]\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]