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.fefc590d48cc : Wed Jun 12 09:39:45 2019 +0200 : correctie or/and in error handling
  • Rev.a96867b4fc09 : Tue Jun 11 17:47:05 2019 +0200 : correction to checkbox handling, was missing some states
  • Rev.f7e97a95f4cf : Tue Jun 11 14:13:05 2019 +0200 : fix to subtable_entries printed as main annotations if empty subtable
  • Rev.caf3b74ca66f : Tue Jun 11 09:20:37 2019 +0200 : add whitespace between variants in PDF reports and correctly break longtable
  • Rev.b6aee75cfa71 : Thu Jun 06 13:28:41 2019 +0200 : Spacing and pagebreak fix in Reports
  • Rev.d2145dc550f2 : Mon May 27 10:09:01 2019 +0200 : reorganise geneUpdates page

Database:

  • Rev.075a6f053404 : Mon May 27 10:03:26 2019 +0200 : store old & new gene name in case of novel transcripts
  • Rev.156d19cff9b5 : Mon May 27 09:38:29 2019 +0200 : added export of updated refLink.tmp (backward update), previous commit only printed refGene.tmp (forward update)
  • Rev.669e8983c810 : Mon May 27 09:22:18 2019 +0200 : Added table to store refGene/refLink discrepancies, and generate a updated refLink.tmp.txt to replace refLink with older gene symbols
  • Rev.7ac99154cd87 : Wed May 22 10:22:12 2019 +0200 : add alamut default build version to the Annotation_Datavalues table
  • Rev.92a42584195d : Thu May 16 20:27:37 2019 +0200 : fixed typo
  • Rev.88d7871884b7 : Thu May 16 20:10:12 2019 +0200 : field to store checkboxes for classifier variants

Click here for full history