WGS Variant Calling - Variant Calling with GATK - Part 1 - Detailed NGS Analysis Workflow
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11
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Overview
Syllabus
Intro
Aim & Intuition behind variant calling
What is GATK?
Somatic vs Germline variants
GATK best practice workflow steps
Data pre-processing steps - alignment
A note on Read Groups
Data pre-processing steps - mark duplicate reads
Data pre-processing steps - Base Quality Score Recalibrator
Variant discovery
Data used for demonstration
System requirements
Setting up directories
Download data
Download reference fasta, known sites and create supporting files .fai, .dict
Setting directory paths
Step 1: Perform QC - FastQC
Step 2: Align reads - BWA-MEM
Step 3: Mark Duplicate Reads - GATK MarkDuplicatesSpark
Step 4: Base Quality Score Recalibration - GATK BaseRecalibrator + ApplyBQSR
Step 5: Post Alignment QC - GATK CollectAlignmentSummaryMetrics and CollectInsertSizeMetrics
Create multiQC report of post alignment metrics
Step 6: Call variants - GATK HaplotypeCaller
Taught by
bioinformagician
Reviews
5.0 rating, based on 1 Class Central review
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This is a wonderfully explained and well-demonstrated short course. Anyone working with the GATK pipeline would know, that there are many reasons behind performing every step. This course shows the steps nicely in a short time.