SV calling using giraffe/vg

[tnnandi]

It's not very clear to me how exactly VG or Giraffe carries out SV calling (if it truly does). The tutorials mention how we can do genotyping using existing SV calls, but I was wondering if VG or Giraffe can actually identify novel SVs in genomes that were not used to construct the VG graph.

The figure in the "Research article summary" page in the Science paper (Dec 2021) has a legend that says "Call variants and genotype", while the title of the article is "Pangenomics enables genotyping of known structural variants in 5202 diverse genomes". The term "known" in the title indicates that the SVs were detected in an upstream step and giraffe used those SV calls for genotyping.

I'd appreciate it if you can clarify if Giraffe can actually do SV calling, or does it use existing calls for generating graphs that can genotype the calls.

[netwon123]

maybe u should use other tools ,like paragraph etc.