If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Where can I get more information about high-throughput sequencing concepts and terms?
This article has been retired, as the resources it cites are somewhat out of date. For an introduction to GATK and sequence analysis, see the Best Practices section of the website, which contains a lot of intro-level information and references useful resources.
We know this field can be confusing or even overwhelming to newcomers, and getting to grips with a large and varied toolkit like the GATK can be a big challenge. We have produced a presentation that we hope will help you review all the background information that you need to know in order to use the GATK:
- Introduction to High-Throughput Sequencing Analysis: all you need to know to use the GATK: slides and video
In addition, the following links feature a lot of useful educational material about concepts and terminology related to next-generation sequencing:
A basic review of the sequencing process.
An excellent, detailed overview of the myriad next-gen sequencing methdologies.
A nice piece explaining the problems inherent in trying to analyze terabytes of data. The GATK addresses this issue by requiring all datasets be in reference order, so only small chunks of the genome need to be in memory at once, as explained here.