I've used samtools for 454 data on coronaviruses, it mirrored what the Roche Newbler software called for the most part and what I'd seen in papers showing data for similar things. I also played around with FreeBayes.
You might be interested in this:
Also see this post:
Was this virus from infected cells, supernatant or a concentrated (e.g. sucrose cushioned) stock? Some (+)ssRNA viruses polyA their genome and their mRNAs, is this the case with you? I'd be interested in seeing how things turn out, I'm working on a similar project.