VariantDB Server Outline

The following options are available throught the menu above:

  1. New Data:
    • Import variants files from the VariantDB FTP server (if enabled)
    • Overview of your data on the ftp server
  2. Variant Filter:
    • Filter Variants from a certain sample using a variety of criteria.
    • Exported results to CSV or produce summary graphs
  3. Manage Samples:
    • Specify sample info such as clinical info, gender, family etc
    • Move samples around to create relevant groups or projects
  4. Manage Projects:
    • Set Permissions on selected groups of samples.
    • Permissions can be set for indivual users or user groups (to be implemented).
  5. Recent Samples:
    • An overview of the last samples you added to the database, still needing initial annotations.
  6. Settings:
    • Overview of the system vesion history
    • Manage Gene Panels
  7. Documentation:
    • System documentation.

Documentation

Use the following links to read quickstart instructions:

IGV Support UPDATED

IGV visualisation is integrated in this website using direct links to load and navigate the variants and reads in IGV. Where possible, VariantDB converts BAM to CRAM. This requires the latest BETA version of IGV. See documentation for full guidelines:

Quick Download links:

  1. Reference genome: http://143.169.238.8/variantdb_files/Genomes/variantdb.genome.zip
  2. IGV-Snapshot: http://software.broadinstitute.org/software/igv/download_snapshot

 

DOCUMENTATION : Here are the full guidelines on how to install and use IGV with our database.

Install VariantDB Locally

VariantDB can be installed locally in two ways:

  1. Use our openbox virtual machine : Instructions
  2. Manually install on your own hardware: Instructions

System Update Log

Web Interface:

  • Rev.e3ccfc81958e : Tue Jan 29 22:25:30 2019 +0000 : Merged in geertvandeweyer/vdb_web-interface_geert/UpdateValidator (pull request #9)
  • Rev.6e7e40e2f462 : Tue Jan 29 22:25:30 2019 +0000 : Close branch UpdateValidator
  • Rev.eb2df034b014 : Thu Jan 24 17:43:15 2019 +0100 : fix to view-clearing for multiple tables
  • Rev.bfa6d3350f2e : Thu Jan 24 17:42:55 2019 +0100 : set path for services from credentials, append to log instead of overwriting
  • Rev.ff7cc5e9cc2e : Thu Jan 24 17:42:00 2019 +0100 : small fix, exit on error
  • Rev.22149d338866 : Thu Jan 24 17:36:33 2019 +0100 : keep log of servicechecker

Database:

  • Rev.134a6c5282d4 : Tue Jan 08 13:44:53 2019 +0100 : fixed typo, wrong variable name.
  • Rev.fc55b53e0abe : Tue Jan 08 09:33:58 2019 +0100 : Trigger update validation on changes and errors
  • Rev.f0d011d8910d : Fri Jan 04 16:07:27 2019 +0100 : Add column to highlight important filters and annotations
  • Rev.0fd7336251c4 : Tue Oct 16 11:17:31 2018 +0200 : applied upstream change
  • Rev.971be1cb2c4d : Tue Oct 16 11:12:41 2018 +0200 : Create tables for gnomad and CADD, download gnomad, exac_AN datatables for annovar, install CADD
  • Rev.236fecca8efc : Tue Sep 18 10:17:20 2018 +0200 : Corrected vid/sid combos updating autoclassified field

Click here for full history