Calling Variants With Mutect

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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.

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

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