Some questions about SV calling

[HuangYihang1222]

Hi Dr Li,
Thank you for developing such a wonderful tool! However, I have some questions about SV calling from the graph:

1.What's the difference between the 2 methods?
(1)Using gfatools bubble to get a bed file like this: gfatools bubble graph.gfa > var.bed
(2)Using minigraph -cxasm --call to get a bed file for each sample like this: minigraph -cxasm --call -t16 graph.gfa sample-asm.fa > sample.bed, then merge them into a total bed file

I wonder what's the difference between the 2 bed file.

2.Must the sample used for SV calling contribute to the graph construction?
If I used 3 samples(A B C and A as the reference) to build a graph, dose this mean I can only call SVs of these samples(A B C or should I exclude A because it's the ref?)? What should I do if I want to call SVs from other samples against the graph?

Thank you,
Yihang Huang