WGS Variant Calling - Variant Calling with GATK - Part 1 - Detailed NGS Analysis Workflow

WGS Variant Calling - Variant Calling with GATK - Part 1 - Detailed NGS Analysis Workflow

bioinformagician via YouTube Direct link

Intro

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1 of 23

Intro

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WGS Variant Calling - Variant Calling with GATK - Part 1 - Detailed NGS Analysis Workflow

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  1. 1 Intro
  2. 2 Aim & Intuition behind variant calling
  3. 3 What is GATK?
  4. 4 Somatic vs Germline variants
  5. 5 GATK best practice workflow steps
  6. 6 Data pre-processing steps - alignment
  7. 7 A note on Read Groups
  8. 8 Data pre-processing steps - mark duplicate reads
  9. 9 Data pre-processing steps - Base Quality Score Recalibrator
  10. 10 Variant discovery
  11. 11 Data used for demonstration
  12. 12 System requirements
  13. 13 Setting up directories
  14. 14 Download data
  15. 15 Download reference fasta, known sites and create supporting files .fai, .dict
  16. 16 Setting directory paths
  17. 17 Step 1: Perform QC - FastQC
  18. 18 Step 2: Align reads - BWA-MEM
  19. 19 Step 3: Mark Duplicate Reads - GATK MarkDuplicatesSpark
  20. 20 Step 4: Base Quality Score Recalibration - GATK BaseRecalibrator + ApplyBQSR
  21. 21 Step 5: Post Alignment QC - GATK CollectAlignmentSummaryMetrics and CollectInsertSizeMetrics
  22. 22 Create multiQC report of post alignment metrics
  23. 23 Step 6: Call variants - GATK HaplotypeCaller

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