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

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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>.'''
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. Also Forqs was written in way with selection experiments in mind, they have functions such as "Quantitative Trait" that allows the user to define the fitness function in a complex way.


* '''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 10:33, 17 October 2013

Analyzing pooled sequenced data with selection <html><img src="/images/9/94/Report.png" border="0" /></html> Main project page
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Simulating evolution and then pooled sequencing

  • We start with a population of N individuals with a certain 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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