What is the best way to generate vcf for vg toolkit from raw sequences

Question

[Sumit]

Hi,

I am trying to generate variation graph (vg) from raw SARS-CoV2 sequences (~16k sequences). What would be the best way to generate VCF given these raw sequences? And, does the method works as the data scales up?

Thanks,

Answer 1

[colindaven]

You can try PGGB for this purpose, since you can enter raw fasta sequences. Not sure if it will scale to that number of genomes though.

https://github.com/pangenome/pggb

It will give you odgi and VCF output, you can further convert from there if needed.