Issue with vg call Generating VCF File for HBV Pangenome

[lihuanhuan20000]

PLEASE DO NOT MAKE SUPPORT REQUESTS HERE
Hello, I used pggb to construct a pangenome for HBV, and then used vg (v1.60.0) to call variants and generate the consensus sequence. However, I encountered some issues.

My commands were as follows:
vg giraffe -Z .giraffe.gbz -m .min -d .dist -f HBV.fastq > sample.gam
vg surject -x .xg sample.gam -b > sample_surjected.bam
vg convert .xg -p > .pg
vg snarls .pg > .snarls
vg pack -x .pg -g sample.gam -o .pack
vg call .pg -r .snarls -k .pack -s sample > sample_all.vcf
The problem is that the generated VCF file contains only one path in the #CHROM column, not all of the paths. However, when I run:
vg call .pg -r .snarls -k .pack -s sample -p path_reference > sample_reference.vcf
it generates the VCF with the corresponding path. If I use -p path1 -p path2, only one path's variant information is output.

I don't understand why the variant information for all paths isn't being generated. Could you please help clarify what might be causing this?

Additionally, since some of my HBV samples are recombinant types, how should I handle consensus sequence generation in such cases? Specifically, how can I manage recombinant variants when generating the consensus sequence?

Thank you!

Please the Biostars forum instead:

https://www.biostars.org/new/post/?tag_val=vg

[glennhickey]

what is the output of vg paths -Lx graph.gbz ?