Create thumbnails of igv.js visualizations and view them all simultaneously in an interactive
igv-grid
Create snapshots of igv.js visualizations of genomic variants and view those thumbnails next to one another in an interactive, responsive web app.
Demo
Note that loci visualizations can be shared with colleagues via URL, e.g., https://igv-grid.surge.sh/0/2 , which refers to thumbnail #2 from callet #0.
Applications
The app was developed to expedite the visual identification of features that differentiate true-positive from false-positive variant calls, such as soft-clipped reads and local sequence context.
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
Installation
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.
Usage
Create thumbnails:
./create-screenshots--build-webapp.sh
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
Customize
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.
Acknowledgements
Web app based upon Travis Horn’s article.
Download Details:
Author: petermchale
Demo: https://igv-grid.surge.sh/
Source Code: https://github.com/petermchale/igv-grid
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