Somatic Variant Calling with Mutect2 - GATK Best Practices Tutorial

Somatic Variant Calling with Mutect2 - GATK Best Practices Tutorial

bioinformagician via YouTube Direct link

Intro

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1 of 22

Intro

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Somatic Variant Calling with Mutect2 - GATK Best Practices Tutorial

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

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