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Best Practices For Variant Calling With The GATK

The presentations below were filmed during the 2013 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 2.6.

Day 1:

   7/9/13 Introduction to NGS for GATK Ryan Poplin PDF Video
   7/9/13 Overview of GATK & best practices Ami Levy-Moonshine PDF Video
   7/9/13 Mapping & marking duplicates Guillermo delAngel PDF Video
   7/9/13 Indel realignment Valentin Ruano-Rubio PDF Video
   7/9/13 Base quality score recalibration Ryan Poplin PDF Video
   7/9/13 Data compression with reduce reads Eric Banks PDF Video

Day 2:

   7/10/13 Calling variants Guillermo del Angel PDF Video
   7/10/13 Variant quality score recalibration Ryan Poplin PDF Video
   7/10/13 Genotype refinement & functional annotation Chris Hartl PDF Video
   7/10/13 Variant manipulation & analysis Chris Hartl PDF Video
   7/10/13 Introduction to parallelism for GATK Mauricio Carneiro PDF Video
   7/10/13 Introduction to Genome STRiP for discovery and genotyping of deletions Bob Handsaker   Video
   7/10/13 XHMM: Discovery and Genotyping of Copy Number Variation from Exome Read Depth Menachem Fromer   Video