vcf_filter command not found

Introduction

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

vcf_filter: command not found

or when using sudo you get the following error message

sudo: vcf_filter: command not found

Solutions to vcf_filter: command not found

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

In Ubuntu vcf_filter is provided by pyvcf package.

pyvcf is:

The Variant Call Format (VCF) specifies the format of a text file used in bioinformatics for storing gene sequence variations. The format has been developed with the advent of large-scale genotyping and DNA sequencing projects, such as the 1000 Genomes Project.

The intent of this module is to mimic the csv module in the Python stdlib, as opposed to more flexible serialization formats like JSON or YAML. vcf will attempt to parse the content of each record based on the data types specified in the meta-information lines – specifically the ##INFO and ##FORMAT lines. If these lines are missing or incomplete, it will check against the reserved types mentioned in the spec. Failing that, it will just return strings.

This package provides helper scripts using python3-pyvcf.

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

sudo apt-get -y install pyvcf

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

You can also use apt command to install pyvcf.

sudo apt -y install pyvcf

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

sudo aptitude install pyvcf

Summary

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