WGS Variant Calling - Variant Filtering and Annotation - Part 2 - Detailed NGS Analysis Workflow
Dive into an in-depth tutorial on variant filtering and annotation using GATK's Funcotator tool in whole genome sequencing (WGS) analysis. Explore the importance of filtering and annotating variants, and learn about two approaches: Variant Quality Score Recalibration (VQSR) and hard filtering. Discover various data sources and the concept of genotype refinement. Follow step-by-step demonstrations on filtering variants at both site and genotype levels, as well as annotating variants with Funcotator. Learn how to process Funcotator output into a tabular format for further analysis and visualization. Gain practical insights into handling VCF files, applying GATK hard-filters for germline variants, and utilizing bioinformatics tools for comprehensive NGS data analysis.