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
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
Recommended Directory Location
Save the scripts to the following directory:
*..\Application Data\Golden Helix SVS\UserScripts\Spreadsheet\Genotype\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, these scripts will be accessible from the Spreadsheet Genotype > Quality Assurance and Utilities menu.
Need a Custom Script?
Need a script and don't feel you have the bioinformatics expertise to write it yourself? Click the link below to request a custom script and we'll see what we can do to help.
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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.