Introduction
In this tutorial we learn how to install bolt-lmm on Ubuntu 20.04.
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 Ubuntu 20.04. 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 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 bolt-lmm using aptitude by running the following command:
sudo aptitude -y install bolt-lmm
How To Uninstall bolt-lmm on Ubuntu 20.04
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 Ubuntu 20.04, 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 Ubuntu 20.04 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
References
Summary
In this tutorial we learn how to install bolt-lmm package on Ubuntu 20.04 using different package management tools: apt, apt-get and aptitude.
