I constructed a graph-based pangenome using a reference FASTA file and a VCF file containing 150 individuals. I used the vg autoindex command with the following script:

sudo chmod -R 777 /tmp

VG=$(which vg)  # or VG=/usr/bin/vg, or unalias vg && VG=$(command -v vg)

fa="ref.fa"

vcf="samples_all.vcf.gz"

prefix="pangenome_graph"

date

echo "Autoindexing the graph..."

$VG autoindex --workflow giraffe \
    --prefix "$prefix" \
    --ref-fasta "$fa" \
    --vcf "$vcf" \
    --threads 4 \

    #-R XG  # Generate an XG index alongside GBZ

echo "Completed autoindexing the graph."

date

However, when I run the following command:

vg gbwt -L -H -Z pangenome_graph.giraffe.gbz

I observed only 17 haplotypes, whereas I expected paths for all 150 individuals. Additionally, I do not see all sample paths in the .gbz and .xg files.

Could you confirm whether these files are suitable for:

1. Short-read mapping using vg giraffe
2. Structural variant calling using vg call

I have attached a screenshot for reference.

Looking forward to your guidance.

Thank you