How To Install vcfanno-examples on Ubuntu
Posted on April 1, 2023 (Last modified on May 20, 2023 )
3 minutes • 441 words
Introduction
In this tutorial we learn how to install vcfanno-examples on Ubuntu.
What is vcfanno-examples
vcfanno-examples 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.
This package contains a test data set as well as sample scripts running some test suite provided by Debian also as autopkgtest.
There are three methods to install vcfanno-examples on Ubuntu. 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-examples 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-examples using apt-get by running the following command:
sudo apt-get -y install vcfanno-examples
Install vcfanno-examples Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install vcfanno-examples using apt by running the following command:
sudo apt -y install vcfanno-examples
Install vcfanno-examples 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 Ubuntu. Update apt database with aptitude using the following command.
sudo aptitude update
After updating apt database, We can install vcfanno-examples using aptitude by running the following command:
sudo aptitude -y install vcfanno-examples
How To Uninstall vcfanno-examples on Ubuntu
To uninstall only the vcfanno-examples package we can use the following command:
sudo apt-get remove vcfanno-examples
Uninstall vcfanno-examples And Its Dependencies
To uninstall vcfanno-examples and its dependencies that are no longer needed by Ubuntu, we can use the command below:
sudo apt-get -y autoremove vcfanno-examples
Remove vcfanno-examples Configurations and Data
To remove vcfanno-examples configuration and data from Ubuntu we can use the following command:
sudo apt-get -y purge vcfanno-examples
Remove vcfanno-examples configuration, data, and all of its dependencies
We can use the following command to remove vcfanno-examples configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge vcfanno-examples
Dependencies
vcfanno-examples have the following dependencies:
References
Summary
In this tutorial we learn how to install vcfanno-examples package on Ubuntu using different package management tools: apt, apt-get and aptitude.