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.460f4d18da92 : Mon Jun 12 10:06:59 2017 +0200 : Update to api to generate BED from a list of genes. Also first files to MaxEntScan integration
  • Rev.bc215e72e642 : Tue May 30 16:16:10 2017 +0200 : small fix to ClinVar Validation Runs
  • Rev.6e99f2bdf5de : Fri May 19 16:03:59 2017 +0200 : Fixed syntax error in UpdateClinvar.pl
  • Rev.565d25501450 : Fri May 19 16:01:45 2017 +0200 : Fixed syntax error in UpdateClinvar.pl
  • Rev.9d78868156cc : Fri May 19 15:48:41 2017 +0200 : Working on revised HGVS syntax
  • Rev.706826fd3126 : Wed Apr 19 12:55:33 2017 +0200 : correction to vcf-output of sample querying.

Database:

  • Rev.8f6d37c3af37 : Fri Feb 17 11:35:10 2017 +0100 : keep track of created databases. Drop them in case of reverting after upgrade failure.
  • Rev.a351eb2fa4f7 : Fri Feb 17 11:25:24 2017 +0100 : corrected invalid default timestamp syntax in 70.sql
  • Rev.752d7ee6578b : Fri Feb 17 09:47:49 2017 +0100 : enable multi-core compilation of R to speed it up.
  • Rev.f0e8f8a767a8 : Fri Feb 17 09:39:36 2017 +0100 : correct mysql syntax to insert spidex license in 60.sql
  • Rev.d8a8e986010e : Fri Feb 17 07:39:12 2017 +0100 : correct field length in ClinVar_XRef_Key to 255. New MYSQL version does not automatically truncate input if too long.
  • Rev.e032b7a926ef : Fri Feb 17 07:07:07 2017 +0100 : correct sql table syntax violating updated mysql versions. Removed non-allowed default value for TEXT column.

Click here for full history