Ahahaha3

hi, Johnsonzcode. What is the size of your genome? How long did 'bwa mem' run?

My Allele.gene.table is exist. But there are many allelic contigs for one chromosome at one position.

Have you solved the problem?

Thanks a lot for your reply!

Do you have resolve the problem? and what's the size of your reference genome?

What does running vg version say?

maybe you can try version=1.38