Create snapshots of igv.js visualizations of genomic variants and view those thumbnails next to one another in an interactive, responsive and collaborative web app.
The app was developed to expedite the visual identification of features that differentiate true-positive from false-positive variant calls, and true-positive from false-negative variant calls.
Aside from methods development, other possible applications may include:
- Sample quality control: identify samples that harbor unusual alignments
- Caller benchmarking: quick visual comparison of the calls made by a set of variant callers
- Collaborative variant interrogation: share a set of variants with colleagues for manual review
Use python 3, e.g.,:
conda create -n igv-grid python=3
conda activate igv-grid
Then download this repo:
git clone https://github.com/petermchale/igv-grid
Then execute:
cd igv-grid
./set-up.sh
Installation successfully tested on Darwin x86_64 and Linux x86_64.
Create thumbnails:
nohup ./create-screenshots--build-webapp.sh > create-screenshots--build-webapp.log 2>&2 &
Start web app:
./launch-web-app.sh
Visit localhost:8080 in your web browser.
If the software is run on a remote machine, then you can view the web-app on a local machine by doing the following from the local machine (change username and host first):
ssh -N -L localhost:8080:localhost:8080 username@host
Alter tracks.json and callSets.json to point to the data you want to visualize. Customize number_thumbnails (number of thumbnails per call set) in create-screenshots--build-webapp.sh.
Another parameter in create-screenshots--build-webapp.sh, named headless_browser_wait_time, represents the length of time puppeteer will wait before taking a screenshot. I've occasionally needed to set this as large as 60000 (1min) to avoid producing incomplete thumbnails.
This is just one example of the difficulties associated with creating screenshots from headless browsers. One solution is to use a service to render thumbnails from the headless browser, e.g., browserless. But a better solution is probably to replace the headless-browser approach with a python tool for creating genomics thumbnails: BamSnap.
Web app based upon Travis Horn's article.