Converting the MutationModel in a TreeSequence

[Julien Y. Dutheil]

Hi,

(I apologize if this was already answered somewhere, in which case a pointer would be very much appreciated :) )

I am combining simulations from SLiM and msprime (deleterious mutations with SLiM, neutral ones with msprime). I use SLiMMutationModel with the sim_mutations function, which works but gives a weird vcf output, as the reference allele is empty and the alternative alleles are mutations ids. Is there any way to convert the mutation alphabet to nucleotides?

Many thanks for your insights,

Julien.

[Jerome Kelleher]

Hi Julien,

This is a timely question! We have an issue open on GitHub to discuss:

https://github.com/tskit-dev/tskit/issues/1341

BTW, this mailing list is being retired in favour of our discussion
boards, https://github.com/tskit-dev/msprime/discussions and
https://github.com/tskit-dev/tskit/discussions

Cheers,
Jerome

> --
> You received this message because you are subscribed to the Google
> Groups "msprime-users" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to msprime-user...@googlegroups.com
> <mailto:msprime-user...@googlegroups.com>.
> To view this discussion on the web, visit
> https://groups.google.com/d/msgid/msprime-users/9ed30458-3daa-4764-a56d-35b10a2cdefdn%40googlegroups.com
> <https://groups.google.com/d/msgid/msprime-users/9ed30458-3daa-4764-a56d-35b10a2cdefdn%40googlegroups.com?utm_medium=email&utm_source=footer>.

[Julien Dutheil]

Dear Jerome,

Thanks a lot! I will switch to GitHub then!

Cheers,

Julien.