search

eblerjana / pangenie

Pangenome-based genome inference
MIT License
102 stars 10 forks source link

Which step used the graph pangenome? #34

Open ttian627 opened 1 year ago

ttian627 commented 1 year ago

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

eblerjana commented 1 year ago

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.