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.a5e580762309 : Thu Apr 12 14:28:50 2018 +0200 : SYNTAX: Added missing bracket in SQL-command
  • Rev.b1ab055cc759 : Thu Apr 12 12:40:13 2018 +0200 : Wait for summary table rebuilds when using novel Variants_x_Users/Projects_Summary tables
  • Rev.3c62a9dc6ec3 : Thu Apr 12 12:38:48 2018 +0200 : BUGFIX: prevent race condition in importer
  • Rev.af72825c1ebb : Thu Apr 12 10:17:31 2018 +0200 : BugFix: added newline to VariantSummary Queued items
  • Rev.9aceb936909d : Thu Apr 12 08:20:05 2018 +0200 : Syntax fixes in VariantDB_PreLoader, API access to shared filters for export
  • Rev.bac2e53f11a5 : Tue Apr 10 22:11:12 2018 +0200 : drop views in excess of 25

Database:

  • Rev.800b77827d31 : Wed Jun 06 12:08:56 2018 +0200 : Correction of saved filters on In_All_Control_Samples; correction of a sift_score format in dbnsfp ; added index on variantID in Variants table
  • Rev.8637558c63b5 : Tue Apr 10 14:19:55 2018 +0200 : Added safety check : drop table if exists
  • Rev.140ad03c1370 : Tue Apr 10 14:12:17 2018 +0200 : Created coverage table for use in summary routines
  • 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

Click here for full history