iVar uses a .tsv file with variants to get the zero based indices (based on the BED file) of mismatched primers. This command requires another .tsv file with each line containing the left and right primer names separated by a tab. This is used to get both the primers for an amplicon with a single mismatched primer. The output is a text file with the zero based primer indices delimited by a space. The output is written to a a text file using the prefix provided.

Documentation can be found at https://andersen-lab.github.io/ivar/html/manualpage.html.