GATK Best Practices Workshop
Date:
11 -15 May 2020
Venue:
JCMB, the Kings' Buildings, the University of Edinburgh, Edinburgh
Places: 30
(first come, first served)
Registration fee:
£120
Information:
The workshop focuses on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. Participants will learn why each step is essential to the variant discovery process, what are the 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 their dataset. In the course of this workshop, we highlight key functionalities such as the GVCF workflow for joint discovery of germline short variants in cohorts, somatic short variant discovery using Mutect2, and somatic copy number variation discovery using GATK-CNV. We also exercise the use of pipelining tools to assemble and execute GATK workflows.
Instructors
GATK - Training team
Workshop format
The term "workshop" is used all over the place to describe very different things. In the GATK world, a workshop is a multi-day course that includes both lectures and hands-on exercises, interleaved to provide a well-balanced learning experience.
Who should attend
This workshop is aimed at a mixed audience of people who are new to the topic of variant discovery or to GATK, seeking an introductory course into the tools, or who are already GATK users seeking to improve their understanding of and proficiency with the tools. Participants should already be familiar with the basic terms and concepts of genetics and genomics. Basic familiarity with the command line environment is required.
Typical workshop schedule
The schedule is given here for a 9am-4pm timeframe but this can be adapted to local needs, e.g. 10am-5pm.
Day 1: Introduction to Genomic Analysis
Morning (9am – 12pm)
- 09:00 Opening remarks
- 09:15 Introduction to sequencing data
- 09:45 Introduction to data pre-processing
- 10:15 Coffee/tea break
- 10:45 Introduction to variant discovery Best Practices
- 11:15 Introduction to pipelining
- 11:45 Closing question time
Lunch Time (12pm – 1pm)
Afternoon (1pm – 4pm)
- 13:00 Orientation to Terra
- 13:30 Case study (part 1)
- 14:30 Coffee/tea break
- 15:00 Case study (part 2)
Day 2: Germline short variant discovery
Morning (9am – 12pm)
- 9:00 Intro to Germline short variant discovery Best Practices
- 9:15 HaplotypeCaller
- 9:45 Joint-calling with GenomicsDB + GenotypeGVCFs
- 10:15 Coffee/tea break
- 10:45 Germline variant discovery tutorial
Lunch Time (12pm – 1pm)
Afternoon (1pm – 4pm)
- 13:00 Germline variant filtering: VQSR and CNN
- 13:30 Genotype Refinement
- 14:00 Callset Evaluation
- 14:15 Coffee/tea break
- 14:45 Germline variant filtering tutorial
Day 3: Somatic variant discovery
Morning (9am – 12pm)
- 9:00 Intro to Somatic variant discovery Best Practices
- 9:15 Somatic SNVs and indels with Mutect2
- 10:00 Coffee/tea break
- 10:30 Somatic SNVs and indels tutorial
Lunch Time (12pm – 1pm)
Afternoon (1pm – 4pm)
- 13:00 Somatic CNVs with GATK-CNV
- 13:30 Somatic CNVs tutorial
- 14:45 Coffee/tea break
- 15:15 Demonstration of upcoming or late-breaking methods
Day 4: Pipelining
Morning (9am – 12pm)
- 9:00 Introduction to pipelining with WDL/Cromwell
- 9:15 Basic pipelining tutorial
- 10:15 Coffee/tea break
- 10:45 Introduction to Docker containers
Lunch Time (12pm – 1pm)
Afternoon (1pm – 4pm)
- 13:00 Advanced pipelining tutorial
- 14:30 Coffee/tea break
- 15:00 WDL puzzles (self-guided exercises)