This is an old revision of the document!
There is a nice introductory wiki to analysis of WES data, a bit outdated, but it is good to understand the basics.
The broad institute has developed GATK, a series of bioinformatic tools to analyze NGS data from the raw files produced by the sequencing service to the files ready for statistical analysis.
As GATK indicates in his Best Practices for Variant Discovery workflow*, WES bioinformatic workflow is divided in three main sections that are meant to be performed sequentially:
* This page displays better with Chrome than with Firefox