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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. 

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