Affymetrix B Allele Frequency Calculation
Author: Greta Peterson, Golden Helix, Inc.
Using Affymetrix CEL files as its source, this script combines quantile normalized SNP A and B probe intensities for each marker into a theta value, then calculates B-Allele Frequencies for each marker.
Affymetrix B Allele Frequency Calculation.py
Recommended Directory Location
Save the script to the following directory:
*..\Application Data\Golden Helix SVS\UserScripts\SVS\Tools
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 SVS Tools menu.
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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.