these are all super minor nits (hope you don't mind!)
* I think SNP should be SNV, since we're not saying anything about population prevalence.
* The "-eval" language is a bit confusing... maybe call these "-include-snv", and "-include-indel"?
* How does args4j allow a user to set a boolean like this to false? (Can you say "-eval-snp false"?) My impression was boolean arguments like this can only be set to true by a user, so would have to default to false