Structural variants

Hi,

This plot has a lot of pre-computed things in there. But the final plotting script you are looking for is here: https://github.com/AsexGenomeEvol/Timema_asex_genomes/blob/main/7_Genome_Alignment/scripts/plot_variants_on_chromosomes.R

In our case, we called SVs using manta (things are explained in methods and with a bit more details but less polished here: https://github.com/AsexGenomeEvol/Timema_asex_genomes/blob/main/6_Structural_Variants/README.md) and filtered with a bunch of criteria. But more importantly, the SVs were always called against a reference genome of the same species.

To get individual references to a common coordinate system, we aligned them to a common chromosomal level reference of one of the species using MUMmer (that is better explained in methods, but all the relevant scripts are here: https://github.com/AsexGenomeEvol/Timema_asex_genomes/tree/main/7_Genome_Alignment). 

So it depends what is you system, if you also have a genus with a stable karyotype and population genomic data for each focal species, you can follow the same trajectory, although I do think some of the methods could be updated these days (e.g. if you have linked or long reads there are better way to call SVs etc).

Anyways, good luck. I hope this helps.

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