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.
BroadE Workshop 2013 Oct 21-22: GATK Best Practices & Queue
The full GATK team presented this workshop at the Broad Institute with support form the BroadE education program.
This workshop included two modules:
Best Practices for Variant Calling with the GATK
The core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. View the workshop materials to learn why each step is essential to the calling process, what are the key operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset.
Building Analysis Pipelines with Queue
An introduction to the Queue pipelining system. View the workshop materials to learn about how to use Queue to create analysis pipelines, scatter-gather them and run them locally or in parallel on a computing farm.