Best Practices For Variant Calling With The GATK
The presentations below were filmed during the 2012 GATK Workshop, part of the BroadE Workshop series. The GATK Workshop covered the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit (GATK), using the “Best Practices” developed by the GATK team.
Workshop topics included the importance of each step to the calling process, 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 a dataset.
Day 1:
| 12/4/12 | Introduction to data processing and variant detection for next-generation DNA sequencing | Eric Banks | Video | |
| 12/4/12 | Introduction to the GATK & GSA best practices | Ami Levy-Moonshine | Video | |
| 12/4/12 | Mapping and duplicate marking | Mauricio Carneiro | Video | |
| 12/4/12 | Indel-based realignment | Eric Banks | Video | |
| 12/4/12 | Base quality score recalibration | Ryan Poplin | Video | |
| 12/4/12 | Data compression with reduce reads | Mauricio Carneiro | Video |
Day 2:
| 12/5/12 | Calling variants |
Guillermo del Angel Ryan Poplin |
Video | |
| 12/5/12 | Variant quality score recalibration | Ryan Poplin | Video | |
| 12/5/12 | Genotype phasing and refinement | Eric Banks | Video | |
| 12/5/12 | Functional Annotation | Eric Banks | Video | |
| 12/5/12 | Analyzing variant calls | Chris Hartl | Video |
