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Calling Variants With Mutect

Learn about how Mutect2 works, and see an example of how to run it in the cloud on Terra. This webinar was originally hosted by the Broad Institute on November 17, 2020, and was open to the GATK community. Presented by Derek Caetano-Anollés, Mark Fleharty, and Brian Haas of the Broad Institute. Follow along with our workshop slides: https://broad.io/GATK2011 Follow along with our Terra workspace: https://app.terra.bio/#workspaces/hel... For more information on GATK, visit https://gatk.broadinstitute.org For more information on Terra, visit https://terra.bio/ OVERVIEW 00:00:00 - Welcome to the webinar 00:02:29 - Mutect2 for somatic SNV and indel discovery 00:06:00 - The fight against false positives 00:11:10 - The almighty Panel of Normals 00:12:41 - Calling variants with Mutect2 00:15:56 - Filtering raw variant calls 00:21:00 - What else can Mutect2 do? DEVELOPER Q&A 00:22:19 - (Q&A) How can I identify somatic variants from cell-free DNA? 00:24:17 - (Q&A) How to prepare a Panel of Normals from my own data 00:24:55 - (Q&A) What to look out for when creating and using PON 00:29:25 - (Q&A) How to increase indel calling accuracy PIPELINE WALKTHROUGH 00:32:30 - Hands-on with Terra 00:34:39 - Preparing our Mutect2 workspace 00:40:04 - Calling somatic SNVs and indels 00:42:55 - Filtering our results 00:48:34 - Using IGV to review our calls 00:51:52 - Annotating our mutations DEVELOPER Q&A 00:55:27 - (Q&A) How does Mutect2 machine learning work? 00:58:27 - (Q&A) What truth data should I use? 01:01:39 - (Q&A) Is it critical for Normal and Tumor datasets to be processed identically? 01:03:09 - Wrapping up the webinar --- Terra is a scalable cloud platform for biomedical researchers to access data, run analysis tools, and collaborate. To learn more about Terra, visit: https://terra.bio/ For documentation, see Terra Support: https://support.terra.bio/hc/en-us For questions, see the Terra community forum: https://support.terra.bio/hc/en-us/co... Subscribe to Terra YouTube: https://www.youtube.com/c/TerraBioApp... TERRA ONLINE Terra App: https://app.terra.bio Terra Support: https://support.terra.bio/hc/en-us YouTube: https://bit.ly/terra-channel Twitter:   / terrabioapp   LinkedIn:   / terrabioapp