Overview
What this challenge is about.
Stand up a Nextflow pipeline covering: read trimming, BWA-MEM alignment, duplicate marking, base-quality-score recalibration, GATK HaplotypeCaller variant calling, and variant filtration. Package each step in a Docker container with pinned versions. Run end-to-end on a 30x-coverage HG002 NA12878 sample (provided), compare resulting VCF against the GIAB v4.2.1 truth set using hap.py, and report precision and recall split by SNP / indel / homopolymer regions. Deliver the pipeline, container images, a 6-page reproducibility README, and the validation report.
The Brief
What you'll do, and what you'll demonstrate.
Replace ad-hoc shell scripts with a containerized, reproducible variant-calling pipeline validated against the GIAB HG002 truth set.
Earning criteria — what you'll demonstrate
- Compose a real bioinformatics pipeline with a workflow manager
- Apply GATK best-practices in a reproducible way
- Validate variant calls against the GIAB truth set
- Communicate reproducibility evidence to academic users
Program Fit
Where this fits in your program.
Sharpens the same skills your degree expects you to demonstrate.
Skills
Skills you'll demonstrate.
Each one shows up on your verified credential.
Careers
Roles this prepares you for.
Real titles. Real skill bridges. Pick the one closest to your trajectory.
Career mappings coming soon.