On December 2, 2021, instructors from the Broad Institute taught a 1-hr virtual webinar open to the GATK community, with guests from Illumina joining to present and and answer questions.

It was hosted by Derek Caetano-Anollés, with additional presentations by Heidi Norton (Illumina) and Michael Gatzen (Broad Institute). Expert panelists from the Broad (Geraldine Van der Auwera and James Emery) and Illumina (Deepthi Shankar) chimed in during the Q&A section to answer questions.

In this webinar, you will learn about the history of the DRAGEN-GATK collaboration, how it works, and how to get started using immediately on the Cloud.

Materials

Follow along with our Terra workspace: https://app.terra.bio/#workspaces/warp-pipelines/DRAGEN-GATK-Whole-Genome-Germline-Pipeline

Visit the Webinar Discussion Topic for this webinar: https://gatk.broadinstitute.org/hc/en-us/community/topics/4410068170779

Agenda & Video

The webinar recording can be found here. Time stamps below may reference specific workshop materials where relevant.

00:00:00 — Welcome to the webinar!
00:02:57 — What's the context
00:08:45 — Bringing DRAGEN to GATK
00:14:09 — Evaluating functional equivalence
00:21:33 — Terra pipeline walkthrough 
00:32:54 — Developer Q&A
00:33:18 — (Q&A) How was DRAGEN-GATK benchmarked?
00:35:00 — (Q&A) How do I do joint-genotyping with DRAGEN-GATK?
00:37:30 — (Q&A) Is DRAGEN-GATK more $$$ than DRAGEN?
00:39:38 — (Q&A) Are there plans to create a GPU-accelerated DRAGMAP?
00:40:18 — (Q&A) Have there been validation done on WES data?
00:42:42 — (Q&A) Does DRAGEN-GATK work for low-coverage data?
00:43:54 — (Q&A) Does DRAGEN-GATK provide forced-genotyping settings?
00:44:54 — (Q&A) Are there plans to expand DRAGEN-GATK to large variants?
00:46:20 — (Q&A) Will the DRAGMAP documentation be expanded?
00:48:15 — (Q&A) Plans to expand DRAGEN-GATK to somatic variants?
00:49:06 — (Q&A) Are results available to view outside Terra?
00:51:10 — (Q&A) What can we expect in the future for DRAGEN-GATK?
00:53:03 — (Q&A) Any comment on panel-seq in DRAGEN-GATK?
00:54:20 — Closing thoughts

Further Resources

For more information on GATK, visit https://gatk.broadinstitute.org

For more information on Terra, visit https://terra.bio/