I am using vg call to get the genotypes of my short-reads. It works well with this parameter:

vg call "$gbz" -k "$pack" "$ref" --sample "$base" --genotype-snarls
--all-snarls --threads 8 > "$base".vcf

However, I noticed that the reference path is alphabetical, wherein the first reference path gets most of the variants:

For example:

variants    chrom
801605  apple
389351  banana
6351    citrus
7309    grapes

I want to get the coordinates of the variants first in the "citrus" reference paths, and then the others. It's so I can easily compare the graph alignment with the linear reference which I have in "citrus" genome, and I also get those variants that are not in the linear ref.

I hope you can help me. Thank you!