If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Attend or host a GATK workshop to see what's cooking
GATK workshops bring you the latest in our methods development. The materials we prepare for workshops often serve as a base for our documentation on new or improved tools and workflows. So not only do GATK workshops cover our established Best Practices, they also give you a taste of what is to come. And let me just say a lot of changes are pouring out of the jar, especially with GATK4.
Let’s get into the logistics of workshops.
Interested in attending a GATK workshop?
Please join the new gatk-workshop group at https://groups.google.com/a/broadinstitute.org/forum/?hl=en#!forum/gatk-workshop to receive emails about upcoming workshops. These emails are different from the group's email updates, so group membership settings should be as shown below with the group Email delivery preference set to Don’t send email updates. You may also browse the posts in the GATK Blog for mention of our workshop schedule.
For information and links for an approaching workshop, we post information on our forum. Look for the announcement box at the top of the GATK Forum homepage. Depending on the hosting institution, a workshop may be open to non-affiliates, and may or may not charge a fee to offset hosting costs.
GATK workshops are by your invitation
We are invited by institutions that then host us. What this means is that, excepting the content that the GATK team brings, all else--the organization and costs--fall to the host. This allows us a workshop schedule that currently averages to a trip approximately every two months. Hosts can coordinate back-to-back workshops in a single trip, as was the case for our Melbourne and Sydney workshops, for cost-effectiveness.
Interested in hosting a GATK workshop?
Contact us by email at [email protected] and provide the following details.
- Your institution name and location.
- Prospective dates, e.g. preferred month(s) and whether you would like the standard two-day workshop or some custom variation.
- Details on the target audience: (i) The approximate number of folks that will attend, (ii) something about their affiliation, e.g. are they from select labs or an entire institution, and (iii) primary research interest, e.g. human or other organisms, somatic or germline research, etc.
Workshop structure can vary
For those who are unfamiliar, hosts typically request a standard two-day workshop. The first day consists of a full day of lectures that detail the latest best practice workflow for germline variant calling and ends with talks on our somatic mutation calling tools. The second day consists of hands-on tutorials aimed at newcomers to GATK tools. We squeeze a lot into the two days. If you want us to cover subjects more deeply or to go at a more relaxed pace, then we can discuss options. We will recommend formulas that are based on our cumulative past experience.
Something for everyone, not just newbs, and a chance to engage us in person
For newcomers to the field, or the tools, the workshop serves as an orientation and can help jump start use of GATK tools. For those already in the know, the workshop improves understanding of (i) why our tools do the things they do, (ii) the power and the limitations of the methods and tools and (iii) what these imply for research. For seasoned experts, a workshop provides an opportunity to ask questions and discuss finer details in person with the communications team and with a GATK methods developer. These discussions happen primarily during the coffee breaks and during the lunch and dinner outings that hosts choose to organize.
Curious about what we present? Browse past workshop materials here. If you pay attention, you’ll notice there is usually something new every workshop either in the talks, the hands-on sections or both.
As always, we appreciate your feedback
When you provide feedback in our forum for our tools or in person at a workshop, we take it seriously. This feedback is integral to improving our methods as well as communication. Please be concrete and constructive in what you feel we can improve, whether bugs or new feature requests. Since our software undergoes iterative improvement, you may see your request fulfilled sooner than you expect in a nightly build or in the next version upgrade.
See how much interest a workshop could garner
GATK has a worldwide user base and this we capture in an interactive map based on ISP locations in this blogpost. If we zoom into the linked map, we resolve regional tallies that the zoomed out map aggregates. Since I have joined the team, we have given workshops in what I would consider regions that are accessible only to a subset of users. The workshops have been in--in reverse chronological order--Boston, Vancouver, Cambridge (UK), Helsinki, Oxford, Edinburgh, Los Angeles, Melbourne, Sydney, Gent (Belgium), Boston, Baltimore and Pretoria (South Africa). If you feel you are missing out, invite us over. It is certainly more cost-effective than sending your scientists to us. Again, contact us by email at [email protected].