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

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(Simulating evolution and then pooled sequencing)
Current revision (12:33, 17 October 2013) (view source)
(Simulating evolution and then pooled sequencing)
 
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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>.'''
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* '''We start with a population of N individuals with a SNP distribution <math> P(M)</math> ~ <math> N(\mu, \Sigma) </math>.'''
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To do this we can use Dick Hudson's MS to lay down neutral variants (but the distribution really does not matter).
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We can use Dick Hudson's MsSel (MS with selection) to generate a SNP distribution.
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* '''We then evolve the populations for g generations with selection for SNP j'''
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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.
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Or, we may have to use [http://arxiv.org/abs/1310.3234 forqs].
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* '''We then evolve the populations for g generations with recombination'''
 
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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>
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Current revision

Analyzing pooled sequenced data with selection Main project page
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Simulating evolution and then pooled sequencing

  • We start with a population of N individuals with a SNP distribution P(M) ~ N(μ,Σ).

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 Pois(λ) where  \lambda \approx 40-50

(2) fi (frequency of the ith SNP) ~  B(n, f_i^{true})



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