cnvkit-reference2targets command not found

Introduction

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

cnvkit-reference2targets: command not found

or when using sudo you get the following error message

sudo: cnvkit-reference2targets: command not found

Solutions to cnvkit-reference2targets: command not found

How To Fix cnvkit-reference2targets: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu cnvkit-reference2targets is provided by cnvkit package.

cnvkit is:

A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from targeted DNA sequencing. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent.

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

sudo apt-get -y install cnvkit

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

You can also use apt command to install cnvkit.

sudo apt -y install cnvkit

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

sudo aptitude install cnvkit

Summary

In this tutorial we learn how to fix cnvkit-reference2targets command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.