cyvcf2 command not found

Introduction

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

cyvcf2: command not found

or when using sudo you get the following error message

sudo: cyvcf2: command not found

Solutions to cyvcf2: command not found

How To Fix cyvcf2: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu cyvcf2 is provided by python3-cyvcf2 package.

python3-cyvcf2 is:

This modules allows fast parsing of VCF and BCF including region-queries with Python. This is essential for efficient analyses of nucleotide variation with Python on high-throughput sequencing data.

cyvcf2 is a cython wrapper around htslib. Attributes like variant.gt_ref_depths return a numpy array directly so they are immediately ready for downstream use.

This package installs the library for Python 3.

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

sudo apt-get -y install python3-cyvcf2

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

You can also use apt command to install python3-cyvcf2.

sudo apt -y install python3-cyvcf2

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

sudo aptitude install python3-cyvcf2

Summary

In this tutorial we learn how to fix cyvcf2 command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.