WGS Variant Calling - Variant Filtering and Annotation - Part 2 - Detailed NGS Analysis Workflow

This tutorial demonstrates hard filtering and genotype refinement for germline SNPs and indels, followed by annotation with GATK Funcotator. It also shows how to convert annotation output into tabular data for further processing and visualization.

Syllabus

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