How To Install snpeff on Debian 12
Introduction
In this tutorial we learn how to install snpeff on Debian 12.
What is snpeff
snpeff is:
“We are all different!” Geneticists agree to this. Even twins, who are said to be identical are on a molecular level only “mostly” identical. And even within the exact same individual, healthy cells acquire mutations such that we are all genetic mosaics. Changes to individual cells may be induced by environmental factors, e.g. like UV light, or happen sporadically as mishaps during cellular divisions.
Because there are so many genetic differences, and most have just no particular meaning for the development of a phenotype, i.e. most have no effect, it would be nice to have heuristics implemented that direct the researcher towards single-nucleotide polymorphisms (SNPs) that are most likely to be relevant. This identifies the gene that causes or contributes to, e.g, an illness, and possibly also genes that are affected by that change. Such mechanistic understanding of a disease, particularly when multiple genes and multiple genetic variants are contributing to the then “polygenic” phenotype, is at the onset of drug development and increasingly also for selecting individualized therapies in the clinic.
SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes). The inputs are predicted variants (SNPs, insertions, deletions and MNPs). The input file is usually obtained as a result of a sequencing experiment, and it is usually in variant call format (VCF).
SnpEff analyzes the input variants. It annotates the variants and calculates the effects they produce on known genes (e.g. amino acid changes).
This package contains the command line tool.
There are three methods to install snpeff on Debian 12. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install snpeff Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install snpeff using apt-get by running the following command:
sudo apt-get -y install snpeff
Install snpeff Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install snpeff using apt by running the following command:
sudo apt -y install snpeff
Install snpeff 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 Debian. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install snpeff using aptitude by running the following command:
sudo aptitude -y install snpeff
How To Uninstall snpeff on Debian 12
To uninstall only the snpeff package we can use the following command:
sudo apt-get remove snpeff
Uninstall snpeff And Its Dependencies
To uninstall snpeff and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove snpeff
Remove snpeff Configurations and Data
To remove snpeff configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge snpeff
Remove snpeff configuration, data, and all of its dependencies
We can use the following command to remove snpeff configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge snpeff
Dependencies
snpeff have the following dependencies:
References
Summary
In this tutorial we learn how to install snpeff package on Debian 12 using different package management tools: apt, apt-get and aptitude.
