snpfilter.sh command not found

Introduction

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

snpfilter.sh: command not found

or when using sudo you get the following error message

sudo: snpfilter.sh: command not found

Solutions to snpfilter.sh: command not found

How To Fix snpfilter.sh: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu snpfilter.sh 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 snpfilter.sh command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.