Alternate Allele Frequency
Author: Mike Thiesen, Golden Helix
This script calculates the percentage of alternate alleles over all samples for each variant. The spreadsheet is expected to have samples as rows and a marker map applied to its columns. The marker map must contain a reference base field.
Recommended Directory Location
Save the script to the following directory:
*..\Application Data\Golden Helix SVS\UserScripts\Spreadsheet\Analysis
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 Analysis menu.
Need a Custom Script?
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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.