GATK Mutect2 Tutorial: Somatic Mutation Calling (Matched Tumor-Normal) — WGS Beginners Guide

🧬 Learn how to detect somatic mutations in cancer using GATK's Mutect2 — the industry gold standard for matched tumor-normal analysis. In this step-by-step tutorial for absolute beginners, we cover the complete pipeline from downloading reference files all the way to a publication-quality table of high-confidence somatic mutations. 📖 Full written tutorial with all code: https://ngs101.com/how-to-analyze-who... ⏱️ TIMESTAMPS: 0:00 Introduction – What Are Somatic Mutations? 2:46 Downloading Somatic-Specific Reference Files 5:24 Setting Up Your Project Directory 6:22 Preparing BAM Files from Part 1 7:21 Running Mutect2 (Tumor-Normal Pair) 10:07 Assessing Sample Contamination 12:06 Filtering Mutations with FilterMutectCalls 13:34 Additional Quality Filters & Summary Stats 15:42 Converting VCF to Human-Readable Tables 👍 If this tutorial helped you, please like, subscribe, and share with your colleagues! 🔔 Subscribe for more bioinformatics tutorials: RNA-seq, ChIP-seq, methylation analysis, and more! #Mutect2 #GATK #SomaticMutation #WGS #CancerGenomics #Bioinformatics #TumorNormalAnalysis #VariantCalling #Genomics #NGS #BioinformaticsTutorial #ComputationalBiology #CancerResearch #NGS101 #WholeGenomeSequencing © NGS Learning Hub | ngs101.com