I am new on vg tools. I have 100+ fungi assemblies and raw reads. The assemblies were aligned by cactus and the output hal file was converted to vg graph by hal2vg. I the vg github page, it seems there was 2 ways to call variants.
mapping reads to the vg graph and use vg call to get variants. Do I need to map the reads of each isolates to graph individually? and get vcfs of each isolates, then merge them together?
use vg deconstruct directly to get the vcf. This seems suitable for my cactus output?
I do not know if my understanding is right? What is the difference of the two methods? Especially for the first method, is it right to map raw reads to graph individually?