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Somatic Variant Calling with Mutect2 - GATK Best Practices Tutorial
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- 1 Intro
- 2 Germline vs Somatic variants
- 3 Germline variant calling vs Somatic variant calling
- 4 Challenges in calling somatic variants
- 5 Overview of somatic variant calling workflow
- 6 Rationale behind Germline Filtering
- 7 Rationale behind Panel of Normals PoN
- 8 Rationale behind Contamination Estimation and Filtering
- 9 Rationale behind Read Orientation Bias
- 10 What questions do somatic variants help to answer?
- 11 Somatic variant databases
- 12 Data used for this demonstration
- 13 Things that will not be covered in this demonstration
- 14 Requirements
- 15 Data download, directory set-up and going over scripts
- 16 Calling variants using Mutect2
- 17 GetPileupSummaries to estimate cross-sample contamination
- 18 Calculate contamination
- 19 Estimate read orientation artifacts
- 20 Filter variants
- 21 Going over filtered variants
- 22 Annotating variants using Funcotator
