Re: [sfscode-users] Simulating a selective sweep

[Ryan H. <rh...@gm...>]

Hi Yang,

You could use something like this:

./sfs_code 1 1 -L 1 10000 -a N --mutation 0 S 5000 G 1000 --trackTrajectory
S 5000 R 1 1 A G 0 -TE 3

This will generate a single locus of length 10kb that is non-coding,
introduce a mutation just after the burn-in at position 5kb with strong
selection coefficient gamma=2Ns=1000, then use the --trackTrajectory option
to follow this particular site until it fixes (R 1 1) automatically
restarting if it is lost by drift (A), and stop the simulation right after
fixation (G 0).  The  -TE 3 is there to keep SFS_CODE running until
fixation.  The value of 3 is just an arbitrarily large number (relative to
expected fixation time) that might as well be 1000.  This seems to be
necessary, and is kind of a bug that I will fix in the next release.

Hope this helps.  Let me know if you have questions.

R

On Thu, Sep 10, 2015 at 10:04 PM, Young <dre...@gm...> wrote:

> Dear Ryan and SFS_CODE'ers,
>
> I have a basic question about SFS_CODE. I want to simulate a selective
> sweep event in a model as following. One segment of sequence of length
> 10000bp under the infinite-site model, and at some time a beneficial allele
> appeared at the midpoint of the sequence, and finally the sample is
> collected at the time of fixation or shortly after the fixation. All the
> mutations should be neutral. It would be appreciated if you could provide
> me the SFS_CODE command line that can simulate such a selective sweep. I
> have read the manual but still not very clear about this.
>
> Best regards,
> Yang
>
>
>
>
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