Calculate Alt Read Ratio between Two Spreadsheets
Author: Autumn Laughbaum, GHI
This tool calculates the ratio of alternate read given an alternate read and reference read spreadsheet. The resulting spreadsheet contains the per-cell ratio as (Alt Depth)/(Alt Depth + Ref Depth) and can be used for filtering purposes with Set Genotypes to No-Call.
Calculate Alt Read Ratio between Two Spreadsheets.py
Recommended Directory Location
Save the script to the following directory:
*..\Application Data\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.
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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.