I have seen this: github.com/vgteam/vg/wiki/Automatic-indexing-for-read-mapping-and-downstream-inference

This thread: github.com/vgteam/vg/issues/3316
seems to be the most comprehensive trail of documentation on how to run, but that seems impossibly difficult to follow.

Same with: github.com/vgteam/vg_snakemake/blob/master/Snakefile

Is there documentation on a simple set of commands like:

vg autoindex ??
vg map $fastqs
vg giraffe $call-set > genotyped-svs.vcf

That I can see to understand the basic steps?

Then it might be feasible for me to understand the workflows.


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