What's the difference of the two parameters (-A and -a) in vg call ?

[dudududu12138]

Hi, I used the latest version of vg. And I noticed that there are 2 parameters -A and -a. The description of them seems similar. I think every and all seems the same? But their might be some different actually. Can you explain? Thank you very much!

vg call -h 
-a, --genotype-snarls   Genotype every snarl, including reference calls (use to compare multiple samples)
-A, --all-snarls        Genotype all snarls, including nested child snarls (like deconstruct -a)

[dudududu12138]

By the way, I use the gbz file and the .xg file of Minigraph Cactus graph to running vg pack and vg call, and I got 2 vcf files. I check the two vcf files are the same. And I ran with/without attaching snarl file, it doesn't seem to have an effect on the results either.

[C-YONG]

Based on my understanding, this option will genotype all snarls, including those nested within other snarls (similar to the behavior of the deconstruct -a command). Nested snarls are variations that occur within larger structural variations (for example, one variation contains another). This option ensures that these nested snarls are also genotyped, even if they are part of a larger structural variation.