Hi developers,

I have a simple question about the VG mpmap. Is VG mpmap able to map reads on multiple regions across the chromosome, not only multi-path?

My question arises from dealing with duplicated genes or high-similarity genes. Is it correct to understand that reads will be aligned on multiple regions and paths if they come from a gene with a high similarity family? Additionally, during the allele-specific quantification with rpvg, after selecting a high score of diploid probability, does the tool calculate the expression values, considering whether the read is multimapped across chromosomes?

Best,