Tumor Copy number variants (CNVs) Identification Using CNVkit — WGS Beginners Guide

Tumor copy number variants — gains and losses of DNA acquired by cancer cells during tumorigenesis — are hallmarks of cancer genomes. They drive aggressive growth, treatment resistance, and therapy response. In Part 6-2 of our Whole Genome Sequencing series for absolute beginners, we extend the CNVkit workflow from Part 6 into the tumor setting. We build a reference exclusively from normal samples, factor tumor purity and ploidy into our calls, split alterations into broad and focal categories, and overlap our results against COSMIC, OncoKB, and ClinVar to bring clinical context to every CNV we find. We also walk through the matched-normal and tumor-only batch modes for production runs. Best watched after Part 6. ⏱ TIMESTAMPS 00:00 Introduction — What Are Tumor (Somatic) CNVs? 02:03 Live RNA-seq Workshop 03:38 Prerequisites & Tumor CNV Workflow 05:38 Setting Up — COSMIC, OncoKB & ClinVar Downloads 07:33 Preparing Your Dataset (Tumor + Normal Samples) 09:24 Building a Tumor-Optimized Reference (Normals Only!) 11:18 Tumor-Normal Copy Number Analysis (Purity & Ploidy) 14:33 Tumor-Specific Filtering — Broad vs Focal CNVs 16:32 Visualization — Scatter, Heatmap & Diagram 18:33 Clinical Interpretation with ClinVar Overlap 21:21 One-Command Analysis — Matched vs Tumor-Only Batch 📖 WRITTEN TUTORIAL (full commands, copy-and-paste ready) https://ngs101.com/how-to-analyze-who... 🎓 LIVE RNA-SEQ WORKSHOP — COHORT 2 (Early-Bird Open) Go from zero command-line experience to a complete, publication-ready RNA-seq pipeline in 7 live, hands-on sessions. Pre-configured cloud environment, no prerequisites, lifetime recordings, and 1 month of email support. Early-bird pricing ends June 14. Seats are limited. 👉 https://ngs101.com/workshop/rna-seq-w... 📺 More free NGS tutorials at NGS101: https://ngs101.com If this helped, please like, subscribe, and comment what you'd like to see next in the WGS series. #Bioinformatics #CancerGenomics #TumorCNV #SomaticCNV #SCNA #CNVkit #WholeGenomeSequencing #WGS #COSMIC #OncoKB #ClinVar #Genomics #NGS #VariantCalling #ComputationalBiology #NGS101