Scripps Genome ADVISER | Annotation and Distributed Variant Interpretation Server

SG-ADVISER UI

The major task in genome interpretation after variant annotation is the identification and/or prioritization of relevant variants. The SG-ADVISER UI utilizes sorting and filtering based upon variant annotations to prioritize variants of interest. The SG-ADVISER UI is a visualization tool for desktop computers that allows investigators of varying computational skill to easily and quickly view, manipulate, sort, filter and extract fragments of the SG-ADVISER output file. Functionality is described in detail below. Download the SG-ADVISER UI .

See Results Description for a description of the content and format of each column.

Example of a annotated file can be found here. Video tutorial can be found here.

Questions, Comments, Suggestions? Post on Biostar.

Running SG-ADVISER UI

OSX users: Double-click SG-ADVISER_UI_'version'.command file to run SG-Adviser UI;
Windows users: Double-click SG-ADVISER_UI_'version'.bat file to run SG-Adviser UI;
Terminal/console/command window users: 'cd' to the folder where the SG-ADVISER UI is located
Type java -Xmx2g -jar SG-Adviser_UI_'version'.jar
You may need more memory, especially if nothing seems to be happening, or you see an error in the terminal/console/command window about "Out of Heap Space". This can be changed by editing the *.command or *.bat file: change "-Xmx2g" to be something larger, like "-Xmx8g" (no quotes). Note that this needs to be lower than your total system memory.


SG-ADVISER UI Visualization Tool

The tool allows you to:

  1. Sort the entire or filtered file by a selected column;
  2. Custom Filters - the custom filters dropdown contains common and suggested filtering strategies. These are presented in the table below:

  3. SG-ADVISER UI Custom Filters

  4. Save - post-filtered annotation data can be saved to file for further manipulation in 3rd party programs. The saved file will include any comments input by the user. The saved file can also be re-loaded later for further manipulation;
  5. Statistics - entire file or filter statistics;
  6. Help Menu;
  7. Simple Filter - string-matched based filtration on a single column directly in the UI interface;
  8. Advanced Filter - the advanced filter button allows filtering using three annotation columns and matched terms;
  9. Undo/Redo - the navigation bar allows the user to undo or redo filtration steps as well as revert to the original data or the last filtration step performed;
  10. Tooltips - if you let the cursor hover above any menu item it will explain its functionality in a few words;
  11. Sort the current view;
  12. Add comments;
  13. Previous/Next pages - scroll through the pages of the view (1000 lines per page);
  14. Load & compare VCF (or Complete Genomics) file - import genotypes from VCF file.

Requirements:

Basic SG-ADVISER UI functionality requires Java JRE 1.5 or newer, but Java JDK 1.6 is recommended (JDK is the full Java Development Kit). Although any operating system with a version of Java should work - this software has been tested on Windows XP and Windows 7, Mac OS X, and Linux.

The tool runs best with a current 64-bit processor, and a 64-bit Java version. The amount of RAM required depends on the size of the file you wish to view. A machine with 2 GB RAM will allow1GB input file; 8GB RAM will allow 4GB file.

Troubleshooting:

Make sure Java is installed. We recommend you have the full Java Developement Kit (JDK) 1.6 installed, and it must be the default version of Java on the system.

You may need more memory, especially if nothing seems to be happening, or you see an error in the terminal/console/command window about "Out of Heap Space". This can be changed by editing the .command or .bat file: Change "-Xmx2g" to be something larger, like "-Xmx8g" (no quotes). Note that this needs to be lower than your total system memory.

Check the forum to see if others encountered your problem or contact at sgadvise@scripps.edu.

Scripps Genome ADVISER | Annotation and Distributed Variant Interpretation Server