Today we will cover Somatic Variant Discovery in more depth. In the morning we primarily focus on calling short variants with Mutect2, and in the afternoon we look at copy number alterations. Both sections have a paired hands-on activity.

• Introduction to Somatic Variant Discovery
• Somatic SNVs and Indels
• Coffee Break
• GATK4 Mutect2 tutorial (hands-on)

• Somatic CNAs
• GATK4 Somatic CNA Tutorial (hands-on)
• Coffee Break
• Mitochondrial Demo