Today we dive deep into the tools that make up the GATK Best Practices Pipeline. In the morning we discuss variant discovery, and in the afternoon we look at refinement and filtering. You will have the opportunity both in the morning and in the afternoon to get hands-on with these tools and run them yourself.

• Introduction to Germline Variant Discovery
• HaplotypeCaller
• Joint Calling
• Coffee Break
• Germline Variant Discovery Tutorial (hands-on)
• Variant Filtration

• Genotype Refinement
• Callset Evaluation
• Coffee Break
• Germline Variant Filtering Tutorial (hands-on)