I have one assembled diploid reference genome in potato and assembled scaffold level polyploid genome in potato, and I want to align both together to call SNP variants. Does anyone have idea which softwares are recommended to do so? Minimap2 seems fine, but there are many called SNPs assigned to multiple chromosomes of reference genome, which is confused to me. Probably this is not the right tool, but is there any tools recommended to do that? Thank you!