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

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Revision as of 21:48, 16 October 2013 by Hussein Alasadi (talk | contribs) (Simulating evolution and then pooled sequencing)
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Simulating evolution and then pooled sequencing

  • We start with a population of N individuals with a certain SNP distribution [math] P(M)[/math] ~ [math] 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 from [math] Pois(\lambda) [/math] where [math] \lambda \approx 40-50 [/math]