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VariantAnalysisPackage

1. Whats included in this installer ?

This installer includes addition/update of the following tools and hundreds of their dependencies;

  1. GATK - tools with a primary focus on variant discovery and genotyping

  2. SURVIVOR - toolset for SV simulation, comparison and filtering

  3. WhatsHap - software for phasing genomic variants

  4. PLINK - association analysis toolset

  5. FreeBayes - bayesian genetic variant detector

  6. FileZilla - opensource FTP client

  7. VEP - Variant Effect Predictor

2. Download Installer

Download the package installer from this link https://molbiocloud.com/help/tiki-download_file.php?fileId=155

3. Prepare for install

3.1. Open a terminal. Move the ‘variantanalysispackage’ installer from your Downloads folder to your home folder using the below command (example screenshot below);

(You can also copy/paste the ‘variantanalysispackage’ installer from Downloads folder to the ‘ubuntu’ home folder, using the Desktop GUI interface, like you will do in a PC or MAC.

cp ~/Downloads/variantanalysispackage .

3.2. Make ‘variantanalysispackage’ installer executable, using the below command (example screenshot below)

chmod 755 variantanalysispackage

 

4. How to run the installer?

Run the script with the following command as example, in your working directory (example screenshot below).

ENTER THE DEFAULT parameters and ‘yes’ for any prompts in the middle of the install. The install would take several 10 minutes.

sudo ./variantanalysispackage

 

The setup assumes that you have not made any system level changes. If the install does not behave as expected, probably the system configuration has been changed. If you face any issues after this update, please let us know ASAP, so that we can help you troubleshoot the issue.

5. Issues ?

If you have any issues with running the installer or need any other information regarding this, please do not hesitate to contact us at contact at molbiocloud.com