Simulations with specified number of segregating sites

[megan...@gmail.com]

Hi everyone,

In Hudson's ms, it was possible to simulate data with a fixed number of segregating sites (the -s option). Is this possible in msprime? Thanks in advance!

Sincerely,

Megan Smith

[Jerome Kelleher]

Hi Megan!

This is something a lot of people ask for. The short answer is "no",
because it's actually quite tricky. Theres's discussion here on github:

https://github.com/tskit-dev/msprime/issues/68

and some further discussion on the list here:

https://groups.google.com/forum/#!searchin/msprime-users/SNP%7Csort:date/msprime-users/Tbr7vnglELs/fDGoeH25CQAJ

Hope this helps!

Cheers,
Jerome

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[Peter Ralph]

Follow-up question: why do you want to do this? (I'm asking to know how to talk about it in the documentation.)

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[megan...@gmail.com]

Thanks, Jerome! That's helpful. Peter, I want to simulate linked SNPs in this case; I just want to simulate data that matches an observed single-locus dataset (mitochondrial sequence) in terms of the number of segregating sites. I think that your suggestion on the last thread (setting the mutation rate high enough and then subsampling) should work fine. Thanks!

Sincerely,

Megan

On Wednesday, March 18, 2020 at 1:45:56 PM UTC-4, Peter Ralph wrote:

Follow-up question: why do you want to do this? (I'm asking to know how to talk about it in the documentation.)

On Wed, Mar 18, 2020 at 10:15 AM Jerome Kelleher wrote:

Hi Megan!

This is something a lot of people ask for. The short answer is "no",
because it's actually quite tricky. Theres's discussion here on github:

https://github.com/tskit-dev/msprime/issues/68

and some further discussion on the list here:

https://groups.google.com/forum/#!searchin/msprime-users/SNP%7Csort:date/msprime-users/Tbr7vnglELs/fDGoeH25CQAJ

Hope this helps!

Cheers,
Jerome



On 18/03/2020 14:53, megan...@gmail.com wrote:
> Hi everyone,
>
> In Hudson's ms, it was possible to simulate data with a fixed number of
> segregating sites (the -s option). Is this possible in msprime? Thanks
> in advance!
>
> Sincerely,
> Megan Smith
>
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> To unsubscribe from this group and stop receiving emails from it, send

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