Version 12 (modified by j.f.j.laros@…, 2 years ago)

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Welcome to project Diagnostic Variant Database (DVD)

Coordinated by the NBIC Bio-Assist program, several groups from Dutch University Medical Centers (LUMC, UMCU, UMCN, UMCG) launched a nation-wide human genomic variant database, the Diagnostic Variant Database (DVD). The purpose is to share all genetic variants detected in the course of next-generation sequencing (NGS) applications between collaborators. This will help medical researchers to distinguish between functionally relevant and benign genetic variants. Therefore, researchers or clinicians can quickly narrow down to those variants that are the potential genetic cause of a particular disease. DVD also allows users to contact the researcher who originally identified a particular genetic mutation. This makes DVD a platform where new research collaboration can be established.

New members are welcome to this shared and closed infrastructure. Please contact the DVD administration team ( dvd-admin) for any membership or technical questions.

Data Access Policy

DVD is a closed system and its content is only available to registered users. Please read the data access policy on how to use DVD.

Source Code Access

The source code of DVD system (Not the data!) is in the public domain and can be used for whatever purpose with absolutely no restrictions. Anonymous readonly subversion access works as follows:

  svn co https://trac.nbic.nl/svn/dvd dvd

Changelog

A list of updates and changes can be found here.

Programs

In the  example client you see how to connect to the database and how to import and annotate your data.

With this  conversion program you can convert a wiggle file to a bed file.

If you have multiple samples that you want to combine into one pool for privacy reasons, you van use this  pooling program. This will convert any number of VCF and Wiggle files into one VCF and multiple BED files.

Use the following  test client to test the webservice (mainly for debugging purposes).

In order to use either one of the clients, you need to rename the file config.py.example to config.py and add your username and password.

More info about either one of these scrips can be obtained by running the script with the -h option.

Test data

We assume that your input data consists of a  VCF and a  wiggle file.

After using the conversion tool mentioned above, you should end up with a  BED file.

Mailing Lists

This project provides the following mailing lists.

  •  dvd-users: a list intended for general discussion on the project.

Advisory Committee

  • Johan den Dunnen (LUMC)
  • Jeroen Laros (LUMC)
  • Joris Veltman (UMCN)
  • Morris Swertz (UMCG)
  • Edwin Cuppen (Hubrecht/UMCU)
  • Victor Guryev (Hubrecht/UMCU)

DVD Administration Team

  • Jeroen Laros (LUMC)
  • Christian Gilissen (UMCN)
  • Robert Wagner (UMCG)
  • Victor Guryev (Hubrecht/UMCU)
  • David van Enckevort (NBIC)
  • Leon Mei (NBIC)

Other NBIC software projects

All active NBIC software projects can be accessed from the  project index.

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