Add-On Script

Find de Novo Candidate Variants

Author: Autumn Laughbaum, GHI

This tool uses pedigree information to identify candidate functional polymorphism, defined as the offspring in a trio having a genotype classified as a Mendelian error. By default, only heterozygous errors are considered candidates. Optionally, homozygous non-reference errors can be considered and require a reference allele field to be present in the marker map. Another option allows the user to restrict computation to affected offspring.

Find de Novo Candidate Variants.pyc

Download Documentation Documentation

Recommended Directory Location

Save the script to the following directory:
*..\Application Data\Golden Helix SVS\UserScripts\Spreadsheet\Quality Assurance

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 Quality Assurance 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.

Python Learning Resources