Puzzle

Note to users and collaborators: We developed Puzzle as an alternative to Scout which would be easy to install and use for anyone. We have since worked a lot with these aspects on the former software and decided to focus our efforts there. Scout features the same SNV and SV views and we are continuing to add features - please check it out: https://github.com/Clinical-Genomics/scout!

Variant Caller GUI and genetic disease analysis tool.

Documentation: https://robinandeer.gitbooks.io/puzzle/content/

$ pip install puzzle
$ wget http://bit.ly/puzzle-bosc
$ unzip puzzle-bosc && rm -r puzzle-bosc
$ puzzle view ./puzzle-demo

Using Puzzle

Puzzle will look for variant calling resources such as VCF files and GEMINI databases and visualize their contents. It lets you inspect, annotate, and analyze variant calls.

Puzzle is not primarily meant to be run as a persistent server but think of it more as an web interface to quickly spin up to visualize variant calls.

We set out to make Puzzle very simple to install and intuitive to use. You should be up and running in minutes with minimal prerequisites.

Developing Puzzle

Puzzle is a Python Flask app with a command line interface. It works with multiple backends using plugins; raw VCFs, GEMINI, MongoDB.

Anyone can help make this project better - read CONTRIBUTING to get started!

Testing Puzzle

To run the tests, you need pytest installed. You can install pytest together with the other development libraries by running pip install -r requirements-dev.txt.

You will also need to download the database used for testing, which you can do by executing this command:

$ wget https://s3-us-west-2.amazonaws.com/robinandeer/HapMapFew.db -O tests/fixtures/HapMapFew.db

To test a GEMINI database with structural variants do:

$ wget https://s3-us-west-2.amazonaws.com/robinandeer/HapMapSv.db -O tests/fixtures/HapMapSv.db

Then, just run py.test tests/

Use ped info

Puzzle uses the PED format to show more information in family view and in variant calls:

$ puzzle view tests/fixtures/hapmap.vcf --family_file tests/fixtures/hapmap.ped

Build documentation

Documentation is generated using Gitbook. Building the docs locally requires the GitBook CLI.

$ cd puzzle/
$ npm install -g gitbook-cli
$ gitbook serve ./docs

The documentation can now be viewed on http://localhost:4000/.

Credits

Puzzle Piece by Creative Stall from the Noun Project

License

MIT. See the LICENSE file for more details.