I need to do a lot of pairwise alignments and obtain a VCF file of each alignment. The purpose of this is to find the mutations between different ORFs of a reference genome and this ORFs in other genomes (one by one). Is there some combination of software that can do this? I am not sure that this can be done with MAFFT or muscle, since they are multiple aligner, and I am not sure that this can be done with a mapper like minimap2 or BWA, since mappers works with reads.
Maybe I could use MAFFT and build a parser in Python to see the mutations in each alignment, but maybe there is a program (or combination of program) that does this more easily.