How To Install vcfanno on Kali Linux

In this tutorial we learn how to install vcfanno on Kali Linux. vcfanno is annotate a VCF with other VCFs/BEDs/tabixed files

Introduction

In this tutorial we learn how to install vcfanno on Kali Linux.

What is vcfanno

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.

There are three methods to install vcfanno on Kali Linux. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install vcfanno Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install vcfanno using apt-get by running the following command:

sudo apt-get -y install vcfanno

Install vcfanno Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install vcfanno using apt by running the following command:

sudo apt -y install vcfanno

Install vcfanno Using aptitude

If you want to follow this method, you might need to install aptitude on Kali Linux first since aptitude is usually not installed by default on Kali Linux. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install vcfanno using aptitude by running the following command:

sudo aptitude -y install vcfanno

How To Uninstall vcfanno on Kali Linux

To uninstall only the vcfanno package we can use the following command:

sudo apt-get remove vcfanno

Uninstall vcfanno And Its Dependencies

To uninstall vcfanno and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove vcfanno

Remove vcfanno Configurations and Data

To remove vcfanno configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge vcfanno

Remove vcfanno configuration, data, and all of its dependencies

We can use the following command to remove vcfanno configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge vcfanno

Dependencies

vcfanno have the following dependencies:

References

Summary

In this tutorial we learn how to install vcfanno package on Kali Linux using different package management tools: apt, apt-get and aptitude.