Building pangenome graphs in minigraph-cactus using vcf?

Question

[Uveyik]

Hi everyone, in the minigraph-cactus pangenome pipeline, normally several fasta files are used. However, I am curious, is there any way to utilize cactus to build pangenome graphs using fasta+vcf?

[Mark]

Not familiar with that tool, but it does sound like you're trying to build a variation graph instead of a reference graph.