In addition to Ram's excellent answer, have a look at bcbio-nextgen and Brad Chapman's blog. The former demonstrates some effective methods for alignment and processing, the later describes a good number of comparisons that you should be familiar with if you want to really get into variant calling pipelines.

Pipelines are built from existing tools. Pipelines are usually customized. You will benefit from reading up on GATK's best practices, and exploring Galaxy documentation on if they have an exome sequencing tutorial.

Probably in need of an update, but not a bad overview of the steps: http://seqanswers.com/wiki/How-to/exome_analysis