I constructed a graph-based pan-genome using 7 chromosome-level genomes with MC, and encountered an issue while calculating the nonreference sequence component supported by minimum haplotypes. I obtained 8 hap-depths. Does this function require a haploid genome to work (since I assembled a diploid genome)? Could this be the cause of the issue?
code：count-vg-hap-cov -p -r T2T -t 30 ../pangenome/fugu.chroms/chr2.vg | less -S
I constructed a graph-based pan-genome using 7 chromosome-level genomes with MC, and encountered an issue while calculating the nonreference sequence component supported by minimum haplotypes. I obtained 8 hap-depths. Does this function require a haploid genome to work (since I assembled a diploid genome)? Could this be the cause of the issue?
code：count-vg-hap-cov -p -r T2T -t 30 ../pangenome/fugu.chroms/chr2.vg | less -S
