vg Giraffe

[pengyan19]

I used VG Giraffe（v1.56.0） to detect variants and found that only variants could be detected up to chromosome 27. Is there a setting for the number of chromosomes in this mode?

[xchang1]

Hi, could you clarify what you're using to detect variants and what reference graph you're using please? And how you built the graph, if you built it yourself. Do you mean that you don't get any reads aligned to chromosome 28?

Giraffe will try to align reads to anywhere in your reference graph, so we don't have a setting for specifying which chromosome to align to.