Varda

Warning

This is a work in progress, probably not yet ready for use!

Varda is an application for storing genomic variation data obtained from next-generation sequencing experiments, such as full-genome or exome sequencing of individuals or populations. Variants can be imported from standard formats such as VCF files and annotated with their frequencies in previously imported datasets.

Varda is implemented as a service exposing a RESTful HTTP interface. Two clients for this interface are under development:

• Manwë - Python client library and command line interface to Varda.
• Aulë - Web interface to Varda.

Please see the tutorial for how to get started with all of these components.

User documentation

This section of the documentation aims to guide users through working with Varda.

• Introduction
  • Use cases
  • Implementation
• User guide
  • Variant frequencies and genomic coverage
  • User roles
  • Sample activation
  • Duplication of data
  • A model for trading data
  • Sample anonymity
  • Pooling samples

Managing Varda

Start here if you’re responsible for getting Varda running on a system.

• Installation
  • If you’re in a hurry
  • Database server: PostgreSQL
  • Message broker and task result backend: Redis
  • Python virtual environment
  • Varda setup
  • Alternative setups
• Upgrading
• Configuration
  • Example configuration
  • Configuration settings
• Running Varda

Tutorial

The tutorial shows you how to setup Varda with the Aulë web interface and Manwë command line client, and how to import and query an example dataset.

• Tutorial
  • Setting up Varda
  • Setting up Aulë
  • Setting up Manwë
  • Importing exome sequencing data
  • Importing aggregate data from 1000 Genomes
  • Querying variant frequencies
  • Annotating variants

REST API documentation

Developers of client applications can read how to communicate with the Varda REST API in this section.

• Introduction to the REST API
  • Conformance with REST
• REST API manual
  • An example request using curl
  • Authentication
  • Passing data with a request
  • Date and time
  • Queries
  • Linked resources and embeddings
  • Collection resources
  • Tasked resources
  • Versioning
  • Error responses
  • Summary of HTTP status codes
• REST API resources
  • API root
  • Authentication
  • Genome
  • Annotations
  • Coverages
  • Data sources
  • Groups
  • Samples
  • Tokens
  • Users
  • Variants
  • Variations

Additional notes

This part contains some notes for developers and other random notes. It needs work, sorry about that.

• Application design
  • Implementation
  • Sample types
  • Frequency calculation
  • Binning of regions and observations
  • Security
  • Sample state
• Todo list
• Changelog
  • Version 0.1.0
• Copyright
  • Authors
  • License
• Links

Indices and tables

• Index
• Module Index
• Search Page