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Away Workshop (Pretoria, SA) 2015 June 22-26: GATK Best Practices and Beyond
Laura Gauthier, Yossi Farjoun and Geraldine Van der Auwera presented this workshop in Pretoria, South Africa, upon invitation from the University of Pretoria.
This workshop covered the core steps involved in calling germline and somatic 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.
Additional considerations were covered, such as 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 sets of hands-on tutorials aiming to teach basic GATK usage to new users, as well as introduce pipelining concepts using Queue.
The workshop was structured into five modules:
- Introductory materials
- Best Practices Phase 1: Pre-processing
- Best Practices Phase 2A: Calling germline variants
- Best Practices Phase 2B: Calling somatic variants
- Best Practices Phase 3: Preliminary analyses
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.