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.20506b0d95eb : Fri Dec 08 16:20:31 2017 +0100 : bugfix samplehandler: syntax error
  • Rev.3a14b7c61d53 : Tue Nov 28 14:16:23 2017 +0100 : use status files instead of hpc job dependencies to wait of tasks to finish
  • Rev.1800d158c6f2 : Mon Nov 27 12:04:38 2017 +0100 : Correction to UpdateClinVar, reactivate actual download
  • Rev.25442847acfd : Mon Nov 27 10:56:05 2017 +0100 : speed optimizations for GenePanel Variant updates
  • Rev.93983fcb1433 : Mon Nov 27 10:12:42 2017 +0100 : Corrections to GO updater, snpEff transcript version reduction to root
  • Rev.77a875b8cb85 : Sun Nov 26 14:00:29 2017 +0100 : restore system before composing update emails. disable mailing for first test

Database:

  • Rev.d79ace15f1f8 : Thu Dec 21 14:17:30 2017 +0100 : create summary tables
  • Rev.af2182ff8ab1 : Thu Dec 14 11:34:05 2017 +0100 : Added Summary tables and Usergroups_GP tables
  • Rev.bb385ae42330 : Tue Dec 12 16:37:43 2017 +0100 : usergroup support
  • Rev.775dc5e7ee02 : Mon Oct 30 11:41:02 2017 +0100 : Second round of index creation. singular aid index is needed for MEMORY tables.
  • Rev.5e8be0496afb : Mon Oct 30 11:38:33 2017 +0100 : Second round of index creation. singular aid index is needed for MEMORY tables.
  • Rev.7d4442917e48 : Fri Oct 27 13:14:19 2017 +0200 : script to add pure vid index on tables.

Click here for full history