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.


Return to top

EADG on 6 Jan 2018


Hi, just to be sure all times are GMT -5 ?

Geraldine_VdAuwera on 6 Jan 2018


Oh yes I forgot to specify, but it is indeed EST, aka GMT-5.

GraceZou on 6 Jan 2018


Chinese users can not access facebook, so could you please share the details of GATK4 livestream in the form of documentation? And when will you come to China to communicate with us for the new version? Sincerely hope your arriving.

Geraldine_VdAuwera on 6 Jan 2018


Hi @GraceZou, we will make the recording available. Organizing a trip to China is not trivial but it will happen; it’s just not clear yet when we will be able. In the meantime we’re looking into doing a webinar specifically for the Chinese community in the near future.

EADG on 6 Jan 2018


Congratulation, you have done it. Thanks for this amazing Software + Support, looking forward to using in upcoming projects. Greetings, EADG




- Recent posts


- Upcoming events

See Events calendar for full list and dates


- Recent events

See Events calendar for full list and dates



- Follow us on Twitter

GATK Dev Team

@gatk_dev

RT @BioCodePapers: GATK PathSeq: A customizable computational tool for the discovery and identification of microbial sequences in libraries…
10 Jul 18
RT @xdopazo: Still some vacancies in the GATK workshop in Seville https://t.co/Wmh8HeqmbY do not miss it! @gatk_dev @ClinicalBioinfo @FProg…
9 Jul 18
Holiday notice: The #GATK forum is on break today as we celebrate US Independence Day. Barring any alien invasion o… https://t.co/IyPKilBhru
4 Jul 18
@StevenNHart @delagoya Thanks for the suggestion, will look into this.
27 Jun 18
@delagoya We could definitely consider that assuming there’s a good way to manage this cleanly. Would love to discu… https://t.co/gNsUNYEXNl
26 Jun 18

- Our favorite tweets from others

Davide Sampietro presenting our work on an #FPGA implementation of the #pairhmm step of the @gatk_dev pipeline by… https://t.co/LU2m4QOtUy
11 Jul 18
@delagoya @gatk_dev Might want to try the builder design pattern for docker. https://t.co/v43xc3Ut0j
26 Jun 18
.@chapmanb shows #bcbio validation graphs: include sensitivity and precision. Compare different tool versions again… https://t.co/OvDXmw6p8x
26 Jun 18
@gatk_dev That’s tough... Thank you so much for maintaining GATK services!
24 Jun 18

See more of our favorite tweets...