User:Hussein Alasadi/Notebook/stephens/2013/10/16: Difference between revisions

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==Simulating evolution and then pooled sequencing==
==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>.'''
* '''We start with a population of N individuals with a 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 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 [http://arxiv.org/abs/1310.3234 forqs].


* '''We then evolve the populations for g generations with recombination'''
To do this we can use Kessner's [http://arxiv.org/abs/1310.3234 Forqs]. Forqs allows the user to specify the recombination rate file which might be useful in the future.


* '''Simulate pooled sequencing'''
* '''Simulate pooled sequencing'''


(1) draw a coverage (n) from <math> Pois(\lambda) </math> where <math> \lambda \approx 40-50 </math>
(1) draw a coverage (n) from <math> Pois(\lambda) </math> where <math> \lambda \approx 40-50 </math>
(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 10:33, 17 October 2013

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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]



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