How To Install bolt-lmm on Kali Linux

In this tutorial we learn how to install bolt-lmm on Kali Linux. bolt-lmm is Efficient large cohorts genome-wide Bayesian mixed-model association testing

Introduction

In this tutorial we learn how to install bolt-lmm on Kali Linux.

What is bolt-lmm

bolt-lmm is:

The BOLT-LMM software package currently consists of two main algorithms, the BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML algorithm for variance components analysis (i.e., partitioning of SNP-heritability and estimation of genetic correlations).

The BOLT-LMM algorithm computes statistics for testing association between phenotype and genotypes using a linear mixed model. By default, BOLT-LMM assumes a Bayesian mixture-of-normals prior for the random effect attributed to SNPs other than the one being tested. This model generalizes the standard infinitesimal mixed model used by previous mixed model association methods, providing an opportunity for increased power to detect associations while controlling false positives. Additionally, BOLT-LMM applies algorithmic advances to compute mixed model association statistics much faster than eigendecomposition-based methods, both when using the Bayesian mixture model and when specialized to standard mixed model association.

The BOLT-REML algorithm estimates heritability explained by genotyped SNPs and genetic correlations among multiple traits measured on the same set of individuals. BOLT-REML applies variance components analysis to perform these tasks, supporting both multi-component modeling to partition SNP-heritability and multi-trait modeling to estimate correlations. BOLT-REML applies a Monte Carlo algorithm that is much faster than eigendecomposition-based methods for variance components analysis at large sample sizes.

There are three methods to install bolt-lmm 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 bolt-lmm Using apt-get

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

sudo apt-get update

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

sudo apt-get -y install bolt-lmm

Install bolt-lmm Using apt

Update apt database with apt using the following command.

sudo apt update

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

sudo apt -y install bolt-lmm

Install bolt-lmm 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 bolt-lmm using aptitude by running the following command:

sudo aptitude -y install bolt-lmm

How To Uninstall bolt-lmm on Kali Linux

To uninstall only the bolt-lmm package we can use the following command:

sudo apt-get remove bolt-lmm

Uninstall bolt-lmm And Its Dependencies

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

sudo apt-get -y autoremove bolt-lmm

Remove bolt-lmm Configurations and Data

To remove bolt-lmm configuration and data from Kali Linux we can use the following command:

sudo apt-get -y purge bolt-lmm

Remove bolt-lmm configuration, data, and all of its dependencies

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

sudo apt-get -y autoremove --purge bolt-lmm

Dependencies

bolt-lmm have the following dependencies:

References

Summary

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