vcfanno command not found

In this troubleshooting guide we learn how to fix vcfanno command not found error message

Introduction

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

vcfanno: command not found

or when using sudo you get the following error message

sudo: vcfanno: command not found

Solutions to vcfanno: command not found

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

In Ubuntu vcfanno is provided by vcfanno package.

vcfanno is:

Vcfanno allows you to quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files. It uses a simple conf file to allow the user to specify the source annotation files and fields and how they will be added to the info of the query VCF.

For VCF, values are pulled by name from the INFO field with special cases of ID and FILTER to pull from those VCF columns.
For BED, values are pulled from (1-based) column number.
For BAM, depth (count), “mapq” and “seq” are currently supported.

Vcfanno is written in go and it supports custom user-scripts written in Lua. It can annotate more than 8000 variants per second with 34 annotations from 9 files on a modest laptop and over 30K variants per second using 12 processes on a server.

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

sudo apt-get -y install vcfanno

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

You can also use apt command to install vcfanno.

sudo apt -y install vcfanno

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

sudo aptitude install vcfanno

Summary

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