Guide Index
Your guide to the Guide

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.

      Best Practices: Official guidelines on how to best use our tools for data processing and analysis
      Tool Documentation: Detailed technical documentation (arguments, options etc.) for each tool
      Methods and Workflows: Recommended methods and typical workflows for multi-step analyses
      FAQs: Frequently Asked Questions
      Tutorials: Tutorials and how-to articles for our tools and pipelines
      Presentations: Materials from live and online events
      Queue: Building analysis pipelines to run GATK and other tools efficiently
      Developer Zone: All you need to know to write your own tools on top of the GATK
      Third-Party Tools: Tools built on top of the GATK developed by other groups

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:

  • Questions, comments? If you have any questions about a specific documentation article, you can post a comment directly on the article in the forum by clicking on the "comment" link that shows up at the beginning and end of each article. Or if you can't find an article that covers the topic you're interested in, you can start your own discussion thread in the forum here.
  • Getting an error/ found a bug? If you're encountering an error while running GATK, or you think you have found a bug, please search the forum to see if anyone else has encountered and reported it already. In many cases, the bug has already been found and fixed, and all you need to do is upgrade to the latest version of GATK. Sometimes it's not even a bug, just a usage error on your part (it happens, especially with complex software like GATK), and someone has already posted a workaround or advice to fix the mistake. But if it looks like your issue is a new bug, then by all means, please report it in the forum here. We just ask that you make sure you've tried running the latest version of GATK and validated your input files before posting. When you do post, we'll need a succinct description of the problem, of the data you're working with, and the command lines that led to the issue.