Galaxy is an excellent option as already suggested. If you want to do it in the cloud Seven Bridges Genomics has an interesting platform and includes some common Exome-Seq pipelines prebuilt. They give you $250 in "startup funds" for running analyses which is enough for several exomes. I've tested three samples and I don't think it even used half of my funds in compute time.

You can use Galaxy with variouse tools if you like. You can install Galaxy locally or use any of the public available ones. GATK2, samtools, snpeff are all available through the Tool Shed.