Day 3 (September, 19th): Somatic variant discovery

Morning (10:45 – 13:45)

  10:45 Recap of somatic variant discovery Best Practices
  11:00 Somatic SNVs and indels with Mutect2
  11:45 Coffee/tea break
  12:15 Hands-on Mutect2

Lunch Time (14:00 – 15:00)

Afternoon (15:15 – 18:15)

  15:15 Somatic CNVs with GATK CNV
  15:45 Hands-on GATK CNV
  17:00 Coffee/tea break
  17:30 Preview of upcoming methods: germline CNV and SV
  18:00 Open question time