Add-On Script

Activate ATCG SNPs to flip strand or exclude SNPs

Activate ATCG SNPs to Flip Strand

Author: Joost W. Morsink and Sander W. van der Laan, University Medical Center Utrecht

This script can be used to identify SNPs that have ambivalent orientation by comparing a genotype dataset with a reference dataset, such as HapMap data. First the script will identify all A/T, T/A, C/G and G/C SNPs where the minor allele in your dataset differs from the minor allele in the reference dataset. Then it will further identify which of those SNPs have a minor allele frequency less than a user-specified value in your dataset. These SNPs will be activated and an active subset will be created. The subset can be used to flip strands before analysis.


Activate ATCG SNPs to flip strand.py

Download Documentation Documentation

Activate ATCG SNPs to Exclude SNPs

Author: Joost W. Morsink and Sander W. van der Laan, University Medical Center Utrecht

This script can be used to identify SNPs that have ambivalent orientation by comparing a genotype dataset with a reference dataset, such as HapMap data. First the script will identify all A/T, T/A, C/G and G/C SNPs where the minor allele in your dataset differs from the minor allele in the reference dataset. Then it will further identify which of those SNPs have a minor allele frequency greater than or equal to 0.40 in your dataset. These SNPs will be activated and an active subset will be created. The subset can be used to exclude the SNPs from the analysis, which had strand orientation that was hard to determine.


Activate ATCG SNPs to exclude SNPs.py

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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