WGS Analysis for Beginners Part 2A: GATK Mutect2 Matched Tumor-Normal Somatic Mutation Calling
Автор: Lei Guo
Загружено: 2026-02-19
Просмотров: 44
Описание:
🧬 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
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#Mutect2 #GATK #SomaticMutation #WGS #CancerGenomics #Bioinformatics #TumorNormalAnalysis #VariantCalling #Genomics #NGS #BioinformaticsTutorial #ComputationalBiology #CancerResearch #NGS101 #WholeGenomeSequencing
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