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

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Revision as of 21:50, 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 ~ .

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 where

(2) (frequency of the ith SNP)