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||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|