Day 2 (September, 18th): Germline short variant discovery

Morning (10:45 – 14:00)

  10:45 Recap of germline variant discovery Best Practices
  11:00 HaplotypeCaller
  11:30 Joint-calling with GenomicsDB + GenotypeGVCFs
  12:00 Coffee/tea break
  12:30 Hands-on joint-calling

Lunch Time (14:00 – 15:00)

Afternoon (15:15 – 18:15)

  15:15 Filtering with VQSR
  15:45 Genotype Refinement
  16:15 Callset Evaluation
  16:30 Coffee/tea break
  17:00 Hands-on filtering approaches