GATK Best Practices and Building Analysis Pipelines with Queue

The presentations below were filmed during the October 2013 GATK Workshop, part of the BroadE Workshop series. At the time of this workshop, the current version of the Broad’s Genome Analysis Toolkit (GATK) was version 2.7.

This workshop included two modules:

Best Practices for Variant Calling with the GATK
The core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. View the workshop materials below to learn why each step is essential to the calling process, what are 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 your dataset.

Building Analysis Pipelines with Queue
An introduction to the Queue pipelining system. View the workshop materials below to learn about how to use Queue to create analysis pipelines, scatter-gather them and run them locally or in parallel on a computing farm. 

Day 1: Best Practices for Variant Calling with the GATK

10/21/13 Introduction to Data Processing
and Variant Detection for Next-Generation DNA Sequencing
Eric Banks PDF Video
10/21/13  Introduction to the GATK
& GSA Best Practices
Ami Levy-Moonshine PDF Video
10/21/13  Mapping and duplicate marking (data pre-processing) Bertrand Haas PDF Video
10/21/13 Indel-based realignment Ami Levy-Moonshine PDF Video
10/21/13  Base quality score recalibration  Eric Banks PDF Video
10/21/13  Data compression with reduce reads David Roazen PDF Video
10/21/13  Calling variants Valentin Ruano-Rubio PDF Video
10/21/13 Variant quality score recalibration Geraldine Van der Auwera PDF Video
10/21/13 Genotype Phasing and Refinement  Geraldine Van der Auwera PDF Video
10/21/13 Functional Annotation Geraldine Van der Auwera PDF Video
10/21/13 Analyzing variant calls Valentin Ruano-Rubio PDF Video
10/21/13 Introduction to Parallelism Mauricio Carneiro PDF Video

Day 2: Building Analysis Pipelines with Queue

10/22/13  Introduction to Queue Mauricio Carneiro PDF Video
10/22/13 Queue 101: The Basics David Roazen PDF Video
10/22/13 Parallelism in Queue Joel Thibault PDF Video
10/22/13 Advanced Queue Usage Khalid Shakir PDF Video