User:Hussein Alasadi/Notebook/stephens/2013/10/16
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(→Simulating evolution and then pooled sequencing) 
(→Simulating evolution and then pooled sequencing) 

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* '''We start with a population of N individuals with a certain SNP distribution <math> P(M)</math> ~ <math> N(\mu, \Sigma) </math>.'''  * '''We start with a population of N individuals with a certain SNP distribution <math> P(M)</math> ~ <math> 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 WF simulation with selection.  
+  
+  
+  Or, we may have to use [http://arxiv.org/abs/1310.3234 forqs].  
  
  
* '''Simulate pooled sequencing'''  * '''Simulate pooled sequencing'''  
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(2) <math> f_i </math> (frequency of the ith SNP) ~ <math> B(n, f_i^{true}) </math>  (2) <math> f_i </math> (frequency of the ith SNP) ~ <math> B(n, f_i^{true}) </math>  
  
  
Revision as of 13:33, 17 October 2013
Analyzing pooled sequenced data with selection  Main project page Previous entry 
Simulating evolution and then pooled sequencing
We can use Dick Hudson's MsSel (MS with selection) to generate a SNP distribution.
In MsSel, we can specify an allele frequency trajectory for a site. We can generate a trajectory based on a simple WF simulation with selection.
(1) draw a coverage (n) from Pois(λ) where (2) f_{i} (frequency of the ith SNP) ~
