Variant calling and anotation in h pylori

Question

[j.roch.lach]

Hello,

I'v got three sequences of genomes (h. pylori wild type, h. pylori mutant with single nucleotide mutation and h. pylori with big deletion (it's exception after experiment)) . I want to call variants and annotate them with amino acids changes. I try to use for these CLC workbench and mapping reads from mutants to de novo assembled wild type genome but i can't add annotation. I annotate the wild type genome with RAST.

Thank you for help!