Whole Exome Sequencing (WES) Beginners Guide - SNV, Mutation Calling, CNV Analysis

Whole Exome Sequencing covers only 1-2% of the genome — but captures ~85% of disease-causing variants. In this tutorial, we walk through the complete WES analysis pipeline for absolute beginners, focusing on the five key differences between WES and WGS: target region setup, WES-specific quality metrics, targeted variant calling, somatic mutation calling with a capture-kit-matched Panel of Normals, and CNV detection with CNVkit. If you've already followed our WGS series, you'll find the workflow familiar — this video zeroes in on exactly what changes, and why. ⏱ TIMESTAMPS 00:00 Introduction — WGS vs. WES vs. Targeted Sequencing 02:24 Live RNA-seq Workshop 03:57 WES vs. WGS — Cost, Coverage, and When to Use Each 06:20 Key Difference #1 — Target Region Setup (BED File & Interval List) 09:10 Key Difference #2 — WES-Specific Quality Metrics (CollectHsMetrics) 12:16 Key Difference #3 — Targeted Variant Calling (HaplotypeCaller with -L) 15:02 Key Difference #4 — Somatic Mutation Calling & Panel of Normals 17:30 Key Difference #4 (cont.) — Running Mutect2 Tumor-Normal Analysis 19:54 Key Difference #5 — CNV Detection with CNVkit 📖 WRITTEN TUTORIAL Full step-by-step tutorial with all commands: https://ngs101.com/how-to-analyze-who... 🎓 LIVE RNA-SEQ WORKSHOP — NGS101 Want hands-on practice with real data and live instructor support? Join our RNA-seq workshop at NGS101 — a structured, beginner-friendly program with a pre-configured cloud environment, lifetime recordings, and 1 month of email support. 👉 https://ngs101.com/workshop/rna-seq-w... 📺 More free NGS tutorials at NGS101: https://ngs101.com If this helped, please like, subscribe, and share with anyone learning bioinformatics. #Bioinformatics #WholeExomeSequencing #WES #WGS #GATK #ExomeAnalysis #VariantCalling #CNVkit #Mutect2 #Genomics #NGS #ComputationalBiology #NGS101 #Exome #PanelOfNormals