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BroadE Workshops

Demand for BroadE workshops is so high that they often fill quickly. To manage demand, we are continuing to increase the number of times we offer our workshops, and we have implemented a one-week registration period for all BroadE workshops. Participants are selected from the pool of applicants who register during this period.

Everyone who registers has an equal chance of being accepted. Registrants are given a priority number at random, and registrants with high priority numbers are put on a participant list. This list may be revised to ensure that BroadE workshops reach a diverse group of Broadies based on the following factors:

  • the applicant’s home institution
  • the applicant’s lab
  • whether the applicant has previously participated in this particular workshop
  • whether the applicant was previously waitlisted for this particular workshop
  • whether the applicant was previously selected to attend this particular workshop and failed to attend without notifying the BroadE organizers

We offer our most popular workshops several times throughout the year. If you are not selected to attend a workshop the first time you register, we encourage you to apply for a future session.


Upcoming Workshops


Image analysis: How to  make an image worth more than a thousand words
Image processing plays a vital role in modern biomedical research. As the capacity to acquire and analyze images continues to grow, so too does CellProfiler, an open-source, freely-downloadable software designed for large-scale, automated phenotypic image analysis. Attendees will have a hands-on practice on CellProfiler as well as brief introduction on related image analysis softwares, followed by case-studies on HCS and cell- type classification.  At the end of the workshop, there will be a breakout session where attendees will receive guidance on analyzing their own image data. If you are curious about automating the analysis of your microscopy data or want to become familiar with "what's possible", come to the workshop and see what's new in CellProfiler v3.
April 3
Registration has closed

Best Practices for Variant Calling with the Genome Analysis Toolkit
This is a four day workshop. Please read the requirements for attendance before signing up.

The workshop focuses on the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit (GATK), 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.

This workshop focuses on calling germline short variants and somatic short variants and copy number alterations with Broad's Genome Analysis Toolkit (GATK), using best practices developed by the DSP Methods development team, who develop GATK. The developers will give talks explaining the rationale, theory, and real-world applications of the GATK Best Practices. You'll learn why each step is essential to the variant-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. If you're an experienced GATK user, you'll gain a deeper understanding of how the GATK works under the hood and how to improve your results further, especially with respect to the latest innovations. The hands-on GATK tutorials in this workshop will be conducted on Terra (, a new platform developed at Broad in collaboration with Verily Life Sciences for accessing data, running analysis tools and collaborating securely and seamlessly. (If you’ve heard of or been a user of FireCloud, think of Terra as the new and improved user interface for FireCloud that makes doing research easier than before!)

All accepted registrants will attend the first day of the workshop. You may select subsequent days à la carte.

Day 1: Thursday, March 21, 2019 — Introductory topics and hands-on tutorials (Required).
We'll start off with introductory lectures on sequencing data, preprocessing, variant discovery, and pipelining. Then you'll get hands-on with a recreation of a real variant discovery analysis in Terra.

Day 2: Friday, March 22, 2019 — Germline short variant discovery (Optional).
Through a combination of lectures and hands-on tutorials, you'll learn: germline single nucleotide variants and indels, joint calling, variant filtering, genotype refinement, and callset evaluation.

Day 3: Tuesday, March 26, 2019 — Somatic variant discovery (Optional).
In a format similar to Day 2, you'll learn: somatic single nucleotide variants and indels, Mutect2, and somatic copy number alterations.

Day 4: Wednesday, March 27, 2019 — Pipelining and additional skills for working in Terra (Optional).
You'll learn how to write your own pipelining scripts in the Workflow Description Language (WDL) and execute them with the Cromwell workflow management system. We will also cover additional skills to help you do an end-to-end analysis in Terra.

March 21-22, 26-27
Registration has closed

Primer on Medical and Population Genetics
The Primer on Medical and Population Genetics series includes informal discussions of basic topics relevant to medical and population genetics by speakers drawn from across the Broad community. The target audience includes technicians, grad students, postdocs, and established investigators just entering the field of complex trait genetics with the goal of bringing all up to speed on basic principles of human genetic variation, genotyping and sequencing methods, statistics, and analysis.

Please note: When the weekly MPG meeting is cancelled (due to weather, conflicting events, etc.), primers are also cancelled.

September - January