How To Install vcfanno on Debian 12
Introduction
In this tutorial we learn how to install vcfanno on Debian 12.
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 Debian 12. 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 first since aptitude is usually not installed by default on Debian. 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 Debian 12
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 Debian 12, we can use the command below:
sudo apt-get -y autoremove vcfanno
Remove vcfanno Configurations and Data
To remove vcfanno configuration and data from Debian 12 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 Debian 12 using different package management tools: apt, apt-get and aptitude.
