At the demo, 'test-variants.vcf' was a regular variation vcf file. I am confused which step used the graph pangenome format with Extended Data Fig. 1. I used the 'pangenome-graph-from-assemblies' pipline to generate a callset.vcf file. What should I do next? Should I use vcfbub to convert it into a bubble file and then perform genotyping?
No need to use vcfbub, this step is only necessary for vcfs produced from the MC graphs. You can use the multiallelic graph vcf produced by the pangenome-from-assemblies pipeline as input for pangenie.
Hello, authors,
At the demo, 'test-variants.vcf' was a regular variation vcf file. I am confused which step used the graph pangenome format with Extended Data Fig. 1. I used the 'pangenome-graph-from-assemblies' pipline to generate a callset.vcf file. What should I do next? Should I use vcfbub to convert it into a bubble file and then perform genotyping?
I would appreciate your help.
Tian Tian