Entering edit mode
6 days ago
PolenP
•
0
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!