Insights on how to "call together" variants across different VCF samples in simulation

[font...@gmail.com]

Hi Ben and everyone.

We have a model that outputs a VCF file (using outputVCFsample for a random sample of individuals of the subpopulation) at 10 different ticks.

Looking at these VCF files separately, they all have a different number of loci retained and, consequently, the ID of these loci vary between the sampling.

Is there a way in SLiM that these could be combined and called together somehow that every VCF would have the same number of loci, all in common? Like one would do when calling variants using empirical data with a ref genome etc.

Another question:

Could we reduce the number of loci sampled?

Say our chromosome has 1000000 positions, if we wanted to produce a VCF file with only 10000 loci, can that be done in SLiM?

Thanks for your time and help.

Cheers

JP

[Ben Haller]

Hi JP!

Neither of these things is supported by SLiM itself, but I'd imagine both would be possible to do with VCF processing software like VCFtools...?  https://vcftools.github.io/index.html  If that software can't do it then you'd need to write your own Python/Perl type of script that does it for you.

Good luck!

Cheers,
-B.

Benjamin C. Haller
Messer Lab
Cornell University


font...@gmail.com wrote on 9/8/25 4:38 PM:

--
SLiM forward genetic simulation: http://messerlab.org/slim/
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