| name | personal-genomics |
| description | Analyse personal DNA / genome files for pharmacogenomics, disease risk, carrier status, ancestry and traits. Use whenever the user mentions DNA or genome analysis, a raw genome file, gene names, drug-gene interactions, or wants to combine multiple DNA sources. |
| disable-agent-invocation | true |
| allowed-tools | Bash Read Glob SendUserFile |
Personal Genomics
Runs the local personal-genomics toolkit over one or more raw DNA files and reports the findings. All analysis is offline; genetic data never leaves the machine.
First: track the workflow
Create a task for each step below, then work them to completion. The run is multi-step and the reporting step (surfacing findings safely) is the one most often skipped once the analysis file is written.
Locate the toolkit
The scripts and their virtualenv live at ~/git/personal-genomics (a .venv/ with pandas/numpy/scipy/reportlab). Use that venv's Python: ~/git/personal-genomics/.venv/bin/python.
If the repo or venv is missing, set it up before analysing:
cd ~/git/personal-genomics && python3 -m venv .venv && .venv/bin/pip install -r requirements.txt
If the toolkit lives elsewhere, ask the user for the path rather than guessing.
Locate the input files
Ask the user where their DNA file(s) are if not already given. Common location is . Supported inputs:
