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.

Intro
Overview of variant calling steps
Questions we may want to ask after calling variants
Variant data sources
Two approaches to filter variants
Hard filtering: Site-level filtering
Hard filtering: Sample-level filtering
Genotype Refinement
Data used for today’s demo
Pre-requisites
Filtering SNPs
Filtering INDELS
Understanding output after filtering FILTER column
Select variants that passed filters
Exclude variants that failed genotype filters
GATK Funcotator tool
Funcotator data sources
Annotate variants using Functotator
Understanding output after annotation Funcotator output
Getting annotations into a tabular format