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.
|7/9/13||Introduction to NGS for GATK||Ryan Poplin||Video|
|7/9/13||Overview of GATK & best practices||Ami Levy-Moonshine||Video|
|7/9/13||Mapping & marking duplicates||Guillermo delAngel||Video|
|7/9/13||Indel realignment||Valentin Ruano-Rubio||Video|
|7/9/13||Base quality score recalibration||Ryan Poplin||Video|
|7/9/13||Data compression with reduce reads||Eric Banks||Video|
|7/10/13||Calling variants||Guillermo del Angel||Video|
|7/10/13||Variant quality score recalibration||Ryan Poplin||Video|
|7/10/13||Genotype refinement & functional annotation||Chris Hartl||Video|
|7/10/13||Variant manipulation & analysis||Chris Hartl||Video|
|7/10/13||Introduction to parallelism for GATK||Mauricio Carneiro||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|