Course schedule
Note
Apart from the starting time the time schedule is indicative. Because we cannot plan a course by the minute, in practice the time points will deviate.
All times are in Berlin time (CEST, UTC+2).
Day 1 — Foundations & Data Preparation (27 April 2026)
| Block | Start | End | Subject |
|---|---|---|---|
| Lecture | 2:00 PM | 2:15 PM | Course introduction |
| Lecture | 2:15 PM | 3:15 PM | Cancer genomics fundamentals, data formats, variant calling overview |
| 3:15 PM | 3:30 PM | BREAK | |
| Setup | 3:30 PM | 3:45 PM | Login, environment check, data setup |
| Exercises | 3:45 PM | 4:40 PM | BAM QC: samtools, flagstat, CollectHsMetrics, MultiQC |
| Discussion | 4:40 PM | 4:55 PM | QC discussion, wrap up |
| Preview | 4:55 PM | 5:00 PM | Preview of Day 2 |
Day 2 — Somatic Variant Calling (28 April 2026)
| Block | Start | End | Subject |
|---|---|---|---|
| Lecture | 2:00 PM | 2:30 PM | Principles of somatic variant detection, Mutect2, filtering, PoN/gnomAD |
| Exercises | 2:30 PM | 3:30 PM | Mutect2 pipeline + FilterMutectCalls + VCF exploration |
| 3:30 PM | 3:45 PM | BREAK | |
| Exercises | 3:45 PM | 4:30 PM | CNVkit analysis |
| Wrap-up | 4:30 PM | 5:00 PM | Review outputs (PASS VCF + CNV results), preview Day 3 |
Day 3 — Variant Annotation & Interpretation (29 April 2026)
| Block | Start | End | Subject |
|---|---|---|---|
| Lecture | 2:00 PM | 2:30 PM | VEP annotation concepts, cancer databases, interpretation strategies |
| Exercises | 2:30 PM | 3:30 PM | Running VEP, filter_vep, ClinVar/REVEL/AlphaMissense |
| 3:30 PM | 3:45 PM | BREAK | |
| Exercises | 3:45 PM | 4:15 PM | VAF analysis: exploring variant allele frequencies in R |
| Exercises | 4:15 PM | 4:45 PM | R analysis: variant visualization and exploration |
| Wrap-up | 4:45 PM | 5:00 PM | Course summary, further resources, bonus material |