On January 9th, 2018, the Broad Institute Data Sciences Platform unleashed the latest version of GATK. GATK4 is completely open source.
This recording of the live launch event is a two-hour whistle-stop tour of what's new and shiny in GATK4. The event features members of the Data Sciences Platform and GATK development team giving short presentations on key features. The event also features panel discussions which dig a bit deeper into the technical underpinnings and implications of these features.
For the panels, our host Geraldine Van der Auwera was 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. You can find a complete synopsis of the event listed below.
Session 1: Performance features (2:00 - 2:30 pm) David Roazan, 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.
For more information on the latest version of GATK visit: https://www.broadinstitute.org/news/broad-institute-releases-open-source-gatk4-software-genome-analysis-optimized-speed-and