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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.

At the time of this workshop, the current version of GATK was version 2.3.

Day 1:

   12/4/12 Introduction to data processing and variant detection for next-generation DNA sequencing Eric Banks PDF Video
   12/4/12 Introduction to the GATK & GSA best practices Ami Levy-Moonshine PDF Video
   12/4/12 Mapping and duplicate marking Mauricio Carneiro PDF Video
   12/4/12 Indel-based realignment Eric Banks PDF Video
   12/4/12 Base quality score recalibration Ryan Poplin PDF Video
   12/4/12 Data compression with reduce reads Mauricio Carneiro PDF Video

Day 2:

   12/5/12 Calling variants Guillermo del Angel
Ryan Poplin
PDF Video
   12/5/12 Variant quality score recalibration Ryan Poplin PDF Video
   12/5/12 Genotype phasing and refinement Eric Banks PDF Video
   12/5/12 Functional Annotation Eric Banks PDF Video
   12/5/12 Analyzing variant calls Chris Hartl PDF Video