Although this is a complicated task, there are some online resources to get you started, for example the SeqAnswers page at http://seqanswers.com/wiki/How-to/exome_analysis and a BioStar thread at http://www.biostars.org/p/1268/

best of luck

If you want to call SNP you could give a look to this guide:

http://link.springer.com/article/10.1007%2Fs00439-012-1213-z/fulltext.html

They analyze human exome data with different tools and softwares.

Hope this helps