How To Install shapeit4 on Kali Linux

In this tutorial we learn how to install shapeit4 on Kali Linux. shapeit4 is fast and accurate method for estimation of haplotypes (phasing)

Introduction

In this tutorial we learn how to install shapeit4 on Kali Linux.

What is shapeit4

shapeit4 is:

Segmented HAPlotype Estimation and Imputation Tools version 4 (SHAPEIT4). SHAPEIT4 is a fast and accurate method for estimation of haplotypes (aka phasing) for SNP array and sequencing data.

There are three methods to install shapeit4 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 shapeit4 Using apt-get

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

sudo apt-get update

After updating apt database, We can install shapeit4 using apt-get by running the following command:

sudo apt-get -y install shapeit4

Install shapeit4 Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install shapeit4 using apt by running the following command:

sudo apt -y install shapeit4

Install shapeit4 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 shapeit4 using aptitude by running the following command:

sudo aptitude -y install shapeit4

How To Uninstall shapeit4 on Kali Linux

To uninstall only the shapeit4 package we can use the following command:

sudo apt-get remove shapeit4

Uninstall shapeit4 And Its Dependencies

To uninstall shapeit4 and its dependencies that are no longer needed by Kali Linux, we can use the command below:

sudo apt-get -y autoremove shapeit4

Remove shapeit4 Configurations and Data

To remove shapeit4 configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge shapeit4

Remove shapeit4 configuration, data, and all of its dependencies

We can use the following command to remove shapeit4 configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge shapeit4

Dependencies

shapeit4 have the following dependencies:

References

Summary

In this tutorial we learn how to install shapeit4 package on Kali Linux using different package management tools: apt, apt-get and aptitude.