Away Workshop (UK) 2015 April 20-24: Best Practices for Variant Calling with GATK
Joel Thibault, Valentin Ruano-Rubio and Geraldine Van der Auwera presented this workshop in Edinburgh, Scotland, and Cambridge, England, upon invitation from the Universities of Edinburgh and Cambridge.
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. The presentation materials describe 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.
Beyond the Best Practices
Additional considerations such as calling variants in RNAseq data and calling cohorts efficiently, as well as dealing with non-human data, RNAseq data, whole-genome vs. exome, basic quality control, and performance.
This was complemented by a set of hands-on exercises aiming to teach basic GATK usage to new users.
The workshop materials are available at this link if you're viewing this post in the forum, or below if you are viewing the presentation page already.