Best Practices for Variant Calling with the GATK

The presentations below were filmed during the March 2015 GATK Workshop, part of the BroadE Workshop series. At the time of this workshop, the current version of Broad’s Genome Analysis Toolkit (GATK) was version 3.3.

This workshop focused on the core steps involved in calling variants with Broad's Genome Analysis Toolkit, using the "Best Practices" developed by the GATK team. View the workshop materials below to gain an understanding of the rationale, theory, and real-life applications of GATK Best Practices. Learn why each step is essential to the calling process, what key operations are 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.

NOTE: The most up-to-date information can be accessed at the GATK website under Best Practices.

03/19/15	Introduction to High-Throughput Sequencing data formats and methods	Joel Thibault	Video
03/19/15	Introduction to the GATK	Geraldine Van der Auwera	Video
03/19/15	Mapping, processing, and duplicate marking with Picard tools	Matt Sooknah	Video
03/19/15	Mapping and processing RNAseq	Ami Levy-Moonshine	Video
03/19/15	Indel realignment	Mark Fleharty	Video
03/19/15	Base quality score recalibration	David Roazen	Video
03/19/15	Introduction to variant discovery: calling cohorts	Louis Bergelson	Video
03/19/15	Variant calling and joint genotyping	Sheila Chandran	Video
03/19/15	Variant quality score recalibration	Bertrand Haas	Video
03/19/15	Introduction to working with variants	Yossi Farjoun	Video
03/19/15	Genotype refinement	Laura Gauthier	Video
03/19/15	Annotation and variant evaluation	David Benjamin	Video