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There is a nice introductory wiki to analysis of WES data, a bit outdated, but it is good to understand the basics.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 bottom.
As GATK indicates, WES workflow is divided in three main sections that are meant to be performed sequentially:
Data cleanup: from raw DNAseq sequence reads (FASTQ files) to analysis-ready reads (BAM files) Variant discovery: from reads (BAM files) to variants (VCF files) Evaluation: callset QC, refinement and preliminary analyses