The Quick Start guide to the GATK is coming soon. In the meantime, the best place to start is the Best Practices section. See also the other tabs this page for tips and advice on navigating the Guide.
The categories menu on the left-hand side shows the top categories under which the documentation articles are classified.
In the unlikely event that the documentation doesn't solve all of your problems, do your holiday shopping and make your coffee too, please use our support forum to get help from a live human. The live human in question will most likely be a member of the GATK development team. However in some cases you may get responses from other people in the GATK user community who are not part of our group. This is usually a good thing, as there are quite a few expert users who we happily trust with answering most questions, and we welcome the help (hurray for free labor). But as with any public forum, we do recommend you exercise judgment in following advice from strangers on the Internet. One thing you can do is check people's role and post count on their public profile.
Now, in practice: