Puzzle

Variant Caller GUI and genetic disease analysis tool.

Overview

Puzzle will look for variant calling resources such as VCF files and GEMINI databases and visualize their content. 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 to visualize your variant calls.

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

When puzzle is installed, in its simplest form it will try to visualize the VCF files in the directory you point to with

$ puzzle view tests/fixtures

Try it!

Annotations

Puzzle will work best if the variants are annotated with VEP or SnpEff, and some additional annotations such as 1000G frequencies and CADD scores.

Gemini support

If the python package GEMINI is installed, the user can visualize a GEMINI database by running

$ puzzle view path/to/geminidatabase.db

Persist information

Even though puzzle is not meant to be persistent, you can still save information in puzzle's database for future querying running. First you need to initialize a puzzle database to store metainformation.

$ puzzle init --root path/to/dir

Default for root is $USER/.puzzle. When one or more databases are created they can be loaded with vcf files and or GEMINI databases.

Loading

VCFs

$ puzzle load /path/to/your/file.vcf

GEMINI databases

$ puzzle load path/to/geminidatabase.db

Developing Puzzle

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

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