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