Somatic Variant Calling with Mutect2 - GATK Best Practices Tutorial

Dive into a comprehensive 38-minute tutorial on somatic variant calling using Mutect2, following GATK's best practices. Explore the differences between germline and somatic variants, understand the challenges in somatic variant calling, and learn about the workflow's key components. Gain insights into germline filtering, Panel of Normals (PoN), contamination estimation, and read orientation bias. Discover the applications of somatic variants in research and familiarize yourself with relevant databases. Follow along with a hands-on demonstration covering data preparation, variant calling with Mutect2, contamination estimation, artifact detection, variant filtering, and annotation using Funcotator. Access provided code repositories and related tutorials to enhance your understanding of bioinformatics techniques in genomic analysis.

Intro
Germline vs Somatic variants
Germline variant calling vs Somatic variant calling
Challenges in calling somatic variants
Overview of somatic variant calling workflow
Rationale behind Germline Filtering
Rationale behind Panel of Normals PoN
Rationale behind Contamination Estimation and Filtering
Rationale behind Read Orientation Bias
What questions do somatic variants help to answer?
Somatic variant databases
Data used for this demonstration
Things that will not be covered in this demonstration
Requirements
Data download, directory set-up and going over scripts
Calling variants using Mutect2
GetPileupSummaries to estimate cross-sample contamination
Calculate contamination
Estimate read orientation artifacts
Filter variants
Going over filtered variants
Annotating variants using Funcotator