How To Install dindel on Debian 9
Introduction
In this tutorial we learn how to install dindel on Debian 9.
What is dindel
dindel is:
Dindel is a program for calling small indels from short-read sequence data (’next generation sequence data’). It currently is designed to handle only Illumina data.
Dindel requires a BAM file containing the read-alignments as input. It then extracts candidate indels from the BAM file, and realigns the reads to candidate haplotypes consisting of these candidate indels. If there is sufficient evidence for an alternative haplotype to the reference, it will call an indel.
It is possible to test indels discovered with other methods using Dindel, for instance longer indels obtained through assembly methods. Dindel will then realign both mapped and unmapped reads to see if the candidate indel is supported by the reads.
Dindel outputs both genotype likelihoods and includes a script to convert these to a VCF file with indel and SNP calls.
There is basic support for outputting realigned BAM files for each realignment-window. These realigned BAM files can be used to call SNPs near (candidate) indels.
There are three methods to install dindel on Debian 9. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Install dindel Using apt-get
Update apt database with apt-get using the following command.
sudo apt-get update
After updating apt database, We can install dindel using apt-get by running the following command:
sudo apt-get -y install dindel
Install dindel Using apt
Update apt database with apt using the following command.
sudo apt update
After updating apt database, We can install dindel using apt by running the following command:
sudo apt -y install dindel
Install dindel 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 dindel using aptitude by running the following command:
sudo aptitude -y install dindel
How To Uninstall dindel on Debian 9
To uninstall only the dindel package we can use the following command:
sudo apt-get remove dindel
Uninstall dindel And Its Dependencies
To uninstall dindel and its dependencies that are no longer needed by Debian 9, we can use the command below:
sudo apt-get -y autoremove dindel
Remove dindel Configurations and Data
To remove dindel configuration and data from Debian 9 we can use the following command:
sudo apt-get -y purge dindel
Remove dindel configuration, data, and all of its dependencies
We can use the following command to remove dindel configurations, data and all of its dependencies, we can use the following command:
sudo apt-get -y autoremove --purge dindel
Dependencies
dindel have the following dependencies:
References
Summary
In this tutorial we learn how to install dindel package on Debian 9 using different package management tools: apt, apt-get and aptitude.