SNP variant analysis

Hello everyone!

I am new in bioinformatics. I have 9 different fungi genomes (8 strains, evolved to have resistance against antifungal drugs + the reference genome). I need to know where are the differencies between the genomes. I have done the “Calling variants in diploid systems” tutorial and read about other methods/tools. Now I’m not sure which one I should use. Can anyone (who do something like that before) recommend a procedure (step by step) for my problem? Or “Calling variants in diploid systems” tutorial is a perfect solution?

Thanks for your support in advance!