snpEff command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

snpEff: command not found

or when using sudo you get the following error message

sudo: snpEff: command not found

Solutions to snpEff: command not found

How To Fix snpEff: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu snpEff is provided by snpeff package.

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.

To fix this problem, we can install more using the command below.

sudo apt-get -y install snpeff

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install snpeff.

sudo apt -y install snpeff

Or if you have aptitude installed you can use the following command.

sudo aptitude install snpeff

Summary

In this tutorial we learn how to fix snpEff command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.