Day 2 · Module 812:10 – 13:00·50 min

Capstone Project

End-to-end mini-analysis on a synthetic dataset: QC → align → call → annotate → interpret.

What this module covers

▸Synthetic FASTQ, VCF, and counts data provided
▸Run the full pipeline against a chr22 reference
▸Present findings to the group

Download .ipynb Solutions notebook Solutions (.ipynb)Synthetic FASTQ Synthetic VCF Synthetic counts

The notebook — live & editable

runs in your browser · no install

Every section's code is already filled in below. Press the ▶ next to any cell (or Shift+Enter) to run it, edit it and run again, or hit Run all to execute the whole notebook top to bottom. No Python or Jupyter install needed — the kernel boots right here in your browser.

Python kernel — not started

first run downloads the runtime (~once, a few seconds)open in full Jupyter ↗

Heads up: this module's pipeline uses command-line tools (e.g. bwa, samtools) that aren't available in the browser kernel. The Python cells run here; tool/shell lines print a note instead.

Loading notebook…