variant calling from reference gene

[wimmulders-ITM]

Hi,
We like to automate our variant calling proces from targeted sanger sequences of genes that our associated to resistance by mapping to a WT (susceptible) reference. Ideally we would like to have a codon based annotation of the variant in case of synonymous or nonsynonymous mutations and nucleotide position in case of indels. (E.g. nonsynonymous Arg60Lys(aac>aag) or other format). Based on the documentation, I assume this is not integrated in to your tool. Could you advise?
Best,
wim