error:[vg::Constructor] Variant/reference sequence mismatch about vg

[adamnovak]

Your VCF file does not match your reference. The VCF thinks that at HiC_scaffold_7:274931 there ought to be the sequence TTTTCAAACAA..., which in some samples can be deleted down to just T. But your FASTA doesn't actually have that sequence there; it has GGAAGGAC... instead.

You should go back to where you got all_sample_sv3.vcf.gz from and figure out why the file you have doesn't actually use your ref.fa as its reference. Maybe one or the other of those files is not the file you meant to use? Or maybe the tool that wrote the VCF is broken?

If the VCF came from a liftover, your liftover method might not be rewriting the REF sequence of the variants to match the target genome, and you should use a different liftover approach that does do that.