We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
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.
GATK4 livestream launch event Tuesday 9 Jan: detailed agenda and speaker lineup
In just a few days, we'll be releasing GATK4 into general availability -- that's right, the big 4.0! To mark the occasion we are hosting a launch event that will be livestreamed on the Broad Institute's Facebook. Here's a short URL if you'd like to share it: broad.io/facebook.
The launch event is going to be a two-hour whistle-stop tour of what's new and shiny in GATK4. My fellow members of the Data Sciences Platform and GATK development team will give short presentations on key features, then we'll have some panel discussions to dig a bit deeper into the technical underpinnings and implications of these features. For the panels we'll be joined by a really exciting lineup of special guests from the University of California Santa Cruz, Yale School of Medicine, Intel, IBM Research, Verily Life Sciences, Amazon Web Services, Cloudera, Alibaba Cloud, and Microsoft Genomics. Details below the fold.
We should also have some time to take questions from the online audience, so be sure to log in and ask your questions in the comments section of the livestream. We'll also be checking the forums and Twitter for those of you who don't have a Facebook account. To be clear, you don't need an account to watch the video stream.
We hope you'll join us to celebrate this important milestone!
Session 1: Performance features (2:00 - 2:30 pm)
David Roazen, lead developer of the GATK4 engine, will present an overview of key performance improvements that make GATK4 tools faster and more scalable. David will then be joined for panel discussions by Laura Gauthier, lead developer of the germline short variant discovery tools in GATK4, and special guests Paolo Narvaez from Intel, Jean-Philippe Martin from Verily Life Sciences, and Marty Lurie from Cloudera.
Session 2: Platforms for running GATK4 (2:30 - 3:00 pm)
Danielle Ciofani, strategic alliances manager for the Broad's Data Sciences Platform, will present options for running GATK4 on-premises and on public cloud platforms, including the Broad's FireCloud analysis portal on Google Cloud. Danielle will then be joined for a lightning round of short presentations by special guests Heshan Li from Alibaba Cloud, Angel Pizarro from Amazon Web Services, Ravi Pandya from Microsoft Genomics, and Frank Liu from IBM Research.
Session 3: Expanded scope of analysis (3:00 - 3:30 pm)
Lee Lichtenstein, associate director of somatic methods development for GATK, will present an overview of the new tools and pipelines available in GATK4 for calling all major classes of variants in germline and somatic exomes and genomes. Lee will then be joined for panel discussions by members of the GATK development team Sam Lee (somatic CNVs), David Benjamin (somatic short variants), Sam Friedman (neural networks for germline filtering) and Mehrtash Babadi (germline CNVs), as well as special guest Eric Banks, director of GATK methods development and one of the original members of the GATK development team.
Session 4: Best Practices pipelines (3:30 - 4:00 pm)
Ruchi Munshi, software engineer in the Broad's Data Sciences Platform, will present an overview of channels used by the GATK team to provide universal access to the Best Practices pipelines, including the Broad's cloud analysis portal, FireCloud. Ruchi will be joined for panel discussions by Jose Soto, fellow software engineer in DSP, and special guests Brian O'Connor of the University of California Santa Cruz, Brad Chapman of the Harvard T.H. Chan School of Public Health and Monkol Lek of Yale School of Medicine.