How To Install varscan on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
2 minutes • 357 words
Introduction
In this tutorial we learn how to install varscan on Ubuntu.
What is varscan
varscan is:
Variant detection in massively parallel sequencing. For one sample, calls SNPs, indels, and consensus genotypes. For tumor-normal pairs, further classifies each variant as Germline, Somatic, or LOH, and also detects somatic copy number changes.
There are three methods to install varscan on Ubuntu. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install varscan Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install varscan using apt-get by running the following command:
sudo apt-get -y install varscan
Install varscan Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install varscan using apt by running the following command:
sudo apt -y install varscan
Install varscan Using aptitude
If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install varscan using aptitude by running the following command:
sudo aptitude -y install varscan
How To Uninstall varscan on Ubuntu
To uninstall only the varscan package we can use the following command:
sudo apt-get remove varscan
Uninstall varscan And Its Dependencies
To uninstall varscan and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove varscan
Remove varscan Configurations and Data
To remove varscan configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge varscan
Remove varscan configuration, data, and all of its dependencies
We can use the following command to remove varscan configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge varscan
Dependencies
varscan have the following dependencies:
References
Summary
In this tutorial we learn how to install varscan package on Ubuntu using different package management tools: apt, apt-get and aptitude.