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.
Mini Workshop (ASHG) 2014 Oct 21: Best Practices for Variant Discovery with GATK
Ami Levy-Moonshine presented this condensed 90-minute workshop given at ASHG 2014 in San Diego, CA on October 21.
This workshop covered all the core steps involved in calling variants with the GATK, using the “Best Practices” developed by the GATK team. The presentation materials outline why each step is essential to the calling process and what are the key operations performed on the data at each step. This includes specific information about variant calling in RNAseq data and efficient analysis of cohorts.
His slide deck is available at this link if you're viewing this post in the forum, or below if you are viewing the presentation page already.
GATK was also featured in another mini-workshop at ASHG which covered the iSeqTools network, focused on cloud-based analysis. The presentation slides will be posted to the iSeqTools website in the near future.
Best Practices for variant discovery in DNA:
Best Practices for variant discovery in RNAseq:
Excerpt from Ami's ASHG poster: