Two resources are now available explaining how to use GBrowse, the Bio::DB::Sam adaptor, and SAMtools to visualize next generation sequence (NGS) data in GBrowse:
GBrowse and Next Generation Sequencing Data
This poster by Scott Cain (and others) explains how to use Bio::DB::Sam and SAMtools with GBrowse 1.70 and GBrowse 2. Previously SAMtools could only be used with GBrowse 2.
GBrowse NGS Tutorial
This step by step tutorial walks you through configuring GBrowse 2 to display data in SAMtools databases. It includes a VMware image to work with, and uses the example human data that is included with SAMtools.
Please let Scott or myself know if you have any questions.
GMOD Help Desk
Recently Galaxy has also added some NGS analysis tools to its collection as well (look down at the bottom left of the tools list). They are in beta, but if you are swamped with this kind of data these might be of use.