created by Geraldine_VdAuwera
on 2017-03-20
This is a summary description of our standard 3-day workshop, with optional 1-day pipelining add-on at the discretion of the organizer.
This workshop formula 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. You 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 your 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 copy number variation discovery using GATK-CNV. Optionally, we can add an extra day to demonstrate the use of pipelining tools to assemble and execute GATK workflows.
Version note: Starting January 2018, all workshops use GATK4 exclusively (no more GATK3).
The workshop is composed of one day of lectures (including many opportunities for Q&A) that is compulsory for all participants, and two days of hands-on training in different analysis use cases, which the host may choose to make optional. This formula can be extended with an additional day of hands-on training focused on pipelining, which can also be made optional by the host.
In the optional hands-on sessions focused on analysis, we walk participants through exercises that teach them how to manipulate the standard data formats involved in variant discovery and how to apply GATK tools appropriately to common use cases and data types. In the course of these exercises, we demonstrate useful tips and tricks for interacting with GATK and Picard tools, dealing with problems, and using third-party tools such as Samtools, IGV, RStudio and RTG Tools.
In the optional hands-on sessions on pipelining, we walk participants through exercises that teach them to write workflow scripts using WDL, the Broad's new Workflow Description Language, and to execute these workflows locally as well as through FireCloud, our publicly available secure cloud-based analysis service.
Participants will perform the exercises on their own laptops. Important note: only MacOS and Linux systems are supported; MS Windows systems are NOT supported.
Please note that this workshop is focused on human data analysis. The majority of the materials presented does apply equally to non-human data, and we will address some questions regarding adaptations that are needed for analysis of non-human data, but we will not go into much detail on those points.
The lecture-based component of the 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. Workshop hosts are encouraged to open the first day of lectures to as many participants as possible.
The hands-on component is aimed at novice to intermediate users who are seeking detailed guidance with GATK and related tools. Basic familiarity with the command line environment is required. Participants will be expected to bring their own laptops with software preinstalled (detailed instructions will be posted two weeks before the course) unless the workshop host provides a computer lab or cloud-based platform. Supported systems are Mac and Unix/Linux systems; MS Windows is NOT supported. Please note that attendance to the hands-on sessions is limited to 30 participants each.
Introductory talks
Germline variant discovery
Updated on 2017-12-24
From jacek_marzec on 2017-05-23
Hi,
do you mind listing the places and dates of workshops in UK in 2017? I’m aware of your workshop in Cambridge (12-14 Jul) and Edinburg (17-19 July), but unfortunately I cannot attend them this time.
Thanks
From shlee on 2017-05-23
Hi @jacek_marzec,
Our upcoming workshops are:
- Cambridge, UK: 7/12-7/14 (Wednesday to Friday)
- Edinburgh, UK: 7/17-7/19 (Monday to Wednesday)
- Helsinki, Finland: 9/13-9/15 (Wednesday to Friday)
- Oxford, UK: 9/18-9/20 (Monday to Wednesday)
Each workshop is three days. The GATK team will present three additional hands-on tutorials on the third day. One of the tutorials is on pipelining with WDL and the other two cover detecting somatic variation using CNV and MuTect2.
We have a Google group that you can join to get emails about upcoming workshops. Sign-up instructions are in [this blogpost](https://software.broadinstitute.org/gatk/blog?id=8622).
From jacek_marzec on 2017-05-24
Thank you @shlee , that’s great.
From jacek_marzec on 2017-05-24
@shlee, do you know which department in Oxford is organising the workshop?
From shlee on 2017-05-25
Sorry @jacek_marzec, I do not.
From jacek_marzec on 2017-08-31
Hi @shlee,
Do you know if the Oxford workshop in September is going ahead?
From Geraldine_VdAuwera on 2017-08-31
@jacek_marzec No, unfortunately the Oxford group had to cancel. Our next workshop in Europe is in Helsinki in September. The following will probably be in Zurich in early 2018. In the meantime we will have workshops in Pretoria, South Africa (October) and Huntington, WV, USA (November). You can see all these on the (newish) Events calendar linked in the top navigation bar.
From jacek_marzec on 2017-08-31
Thanks @Geraldine_VdAuwera. The Zurich workshop sounds interesting. The Events calendar is very useful, thanks for the hint.