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

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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) ~ 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 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.
 
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* '''Simulate pooled sequencing'''
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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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* '''Simulate pooled sequencing'''
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(1) draw a coverage (n) from <math> Pois(\lambda) </math> where <math> \lambda \approx 40-50 </math>
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(2) <math> f_i </math> (frequency of the ith SNP) ~ <math> B(n, f_i^{true}) </math>

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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