There are many good resources to learn about analyzing NGS data. I suggest you start browsing them before posting open ended questions. One example: http://bcbio.wordpress.com/tag/galaxy/

I reccomend that you get in touch with a more experienced researcher and try to coin the scientific problem and the desired analysis much better. To be honest, asking for "the best pipeline for XYZ" and choosing a tool without having framed the problem is in itself proof of lack of scientific question or communication in the lab; definitely asking for trouble.

As the other comments point out. This question is far too broad for us to answer. What kind of human whole genome sequence data will you be getting? What is the nature of the biological question you are trying to answer? I.e., are they tumor-normal comparisons, blood samples from families with genetic disorder, etc? What kind of sequencing was done (Illumina or some other platform) and to what average coverage? What kind of analysis are you hoping to do? I.e., Are you hoping to find SNVs, Indels, CNVs, SVs, etc. These details and more will all have an impact on determining the "best pipeline" for analysis.