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>.''' | ||
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]. | |||
* '''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 <html><img src="/images/c/c3/Resultset_previous.png" border="0" /></html>Previous entry<html> </html> |
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 W-F simulation with selection.
(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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