Annotate and Filter Variants
Author: Greta Peterson, Andrew Jesaitis, Golden Helix, Inc.
This script will annotate and filter variants based on information found in Variant, Interval, and Gene sources. Filters can be chained together and spreadsheets will be output at each level of the filter chain.
Recommended Directory Location
Save the script to the following directory:
*..\Application Data\Local\Golden Helix SVS\UserScripts\Spreadsheet\DNA_Seq\
Note: The Application Data folder is a hidden folder on many operating systems and its location varies between operating systems. The easiest way to locate this directory on your computer is to open SVS and go to Tools >Open Folder > UserScripts Folder. If saved to the proper folder, this script will be accessible from the Spreadsheet DNA-Seq menu.
Need a Custom Script?
Need a script and don't feel you have the bioinformatics expertise to write it yourself? Click the link below to request a custom script and we'll see what we can do to help.
Request Custom Script »
What is Python?
Python is a clear and powerful object-oriented programming language, comparable to Perl, Ruby, Scheme, or Java. Integrating Python into SVS provides full programmatic access to many of the software's features enabling the augmentation of existing tools, creating entirely new ones, automation of work flows, integration with other programs and more.