I performed Giraffe alignment to map reads to the HPRC pangenome, resulting in a gam file. Subsequently, I utilized the following commands to generate a .vcf file: Generated a pack file with the following command:

./vg pack –x hprc-v1.0-mc-grch38-minaf.0.1.gbz –g hprc1004mapped.gam > hprc1004.aln.pack

Created the .vcf file using this command:

./vg call hprc-v1.0-mc-grch38-minaf.0.1.gbz –a –r hprc-grch38.snarls.pb –k hprc1004.aln.pack > hprc1004.vcf

Upon inspecting the file using a text editor, the contents appear to be in order. I proceeded to generate a .tbi file using the tabix command:

Tabix-p vcf hprc1004.vcf.gz

However, despite attempting to view the vcf in IGV version 2.16.2, no variants are visible ("No Variant Found" appears in the vcf track). I've tried zooming in extensively and even navigating to locations where variants are listed in the text editor, yet I cannot observe any variants in IGV.