How To Install bio-vcf on Debian 12
Introduction
In this tutorial we learn how to install bio-vcf on Debian 12.
What is bio-vcf
bio-vcf is:
Bio-vcf provides a domain specific language (DSL) for processing the VCF format. Record named fields can be queried with regular expressions, e.g.
sample.dp>20 and rec.filter !~ /LowQD/ and rec.tumor.bcount[rec.alt]>4
Bio-vcf is a new generation VCF parser, filter and converter. Bio-vcf is not only very fast for genome-wide (WGS) data, it also comes with a really nice filtering, evaluation and rewrite language and it can output any type of textual data, including VCF header and contents in RDF and JSON.
There are three methods to install bio-vcf 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 bio-vcf Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install bio-vcf using apt-get by running the following command:
sudo apt-get -y install bio-vcf
Install bio-vcf Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install bio-vcf using apt by running the following command:
sudo apt -y install bio-vcf
Install bio-vcf 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 bio-vcf using aptitude by running the following command:
sudo aptitude -y install bio-vcf
How To Uninstall bio-vcf on Debian 12
To uninstall only the bio-vcf package we can use the following command:
sudo apt-get remove bio-vcf
Uninstall bio-vcf And Its Dependencies
To uninstall bio-vcf and its dependencies that are no longer needed by Debian 12, we can use the command below:
sudo apt-get -y autoremove bio-vcf
Remove bio-vcf Configurations and Data
To remove bio-vcf configuration and data from Debian 12 we can use the following command:
sudo apt-get -y purge bio-vcf
Remove bio-vcf configuration, data, and all of its dependencies
We can use the following command to remove bio-vcf configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge bio-vcf
Dependencies
bio-vcf have the following dependencies:
References
Summary
In this tutorial we learn how to install bio-vcf package on Debian 12 using different package management tools: apt, apt-get and aptitude.