We don't use GATK much, but yes, it works just fine for that (honestly, they're all about the same, it's mostly a matter of how you prefer to structure things). If you're primarily interested in GATK, though, you should consider bcbio-nextgen. Brad Chapman has put a good bit of work into tuning bcbio to make variant calling a bit faster (have a look at his blog, which is generally useful if you're doing variant calling).