Update tutorial for new VariantData format #945
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hyanwong
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Using existing data set is a good call. The tooling isn't there yet, I don't think there's much point in trying to force it through for this PR. |
Hmm, is that true? I don't really know what a VCF looks like (and I don't really want to learn about it either). At least for teaching, it's clearer to me to start with a set of alignments (i.e. haplotype data), not site-by-site data, which as a biologist, I always find slightly more confusing to deal with. For example, when storing viral genomes, I think of the sequence of the virus, not the variation at each site. Surely that's more of a natural thing to think about, biologically? Anyway, the SGkit stuff is removed now, and I think it all still reads fine. Maybe we can merge (once it's building properly) and iterate from there? It would be useful for teaching to have examples which work using the new input format. |
No python tabix writer available. This can be removed when we have a tskit2zarr utility.
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Hopefully will force a re-run
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Finally got this to build: that was a bit of a marathon. I think we can merge this, and also close #865 which I had to roll into this PR to get it to build properly. |
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P.s. happy to squash all these commits together, if that helps. |
This allows us to reserve the word "tutorial" for more specific inference tutorials, for example, on the tutorials site. It's also more accurate: people are more likely to just straight to e.g. the VCF usage section rather than work their way through the whole page.
First pass at changing the tutorial to match the new VariantData format. Based off #944
I haven't sorted out the population specification in the sparrows data example yet