Tutorials
From Statistical Genetics Courses
Contents
Running Tutorials on Your Computer
We have created a debian repository to make it easier to use our tutorials. Using this repository will require that you have administrator access to the computer with Linux System. If you don't have this level of access or your computer running non-Linux systems (Windows or OS), you have two options. First, you could install the repository on a remote cloud serve, such as VULTR. Second, you can install a Virtual Machine program (such as VirtualBox) on your computer, and then load our pre-configured virtual machine image (VM Image) into the Virtual Machine.
The VM Image is available here. The password for the student account is "LetMeIn". Feel free to change it to whatever you like.
To install the repository on the cloud server, virtual machine, or your own computer, you need to follow these configuration steps. Please run as the root user or using the sudo command.
echo "deb [trusted=yes] https://statgen.research.bcm.edu/deb ./" | sudo tee -a /etc/apt/sources.list.d/statgen.list sudo add-apt-repository ppa:webupd8team/java sudo apt-get update
If you want to install all below exercises, you could use the following command. In addition, you could also install these exercise separately using specific commands listed in each section below.
the command to install all
Annotation
Functional Annotation Exercise [PDF]
Cochran Armitage Trend Test
GATK and IGV
Software Links
Result Files
GenABEL
GWAS: Data Quality Control
Installing Packages
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install plink-tutorial
The exercise's files will then be installed in the folder /home/shared/Plink_DataQC. You can run from there or copy the files into your user's home directory and proceed with the exercise.
GWAS: Association Analysis Controlling for Population Substructure
Installing Packages
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install plink-tutorial
The exercise's files will then be installed in the folder /home/shared/Plink_substructure. You can run from there or copy the files into your user's home directory and proceed with the exercise.
Regression
RV-TDT
Installing Packages
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install rvtdt-tutorial
The exercise's files will then be installed in the folder /home/shared/rvtdt. You can run from there or copy the files into your user's home directory and proceed with the exercise.
Population Genetics
PSEQ
SEQSpark
Installing Packages
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install seqspark-tutorial
The exercise's files will then be installed in the folder /home/shared/seqspark. You can run from there or copy the files into your user's home directory and proceed with the exercise.In order for the commands to work correctly, you don't need to reboot, but you should log out and log back in to make sure that the computer's environment is correctly configured.
Variant Association Tools
Installing Packages
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install vtools-tutorial
The exercise's files will then be installed in the folder /home/shared/vat. You can run from there or copy the files into your user's home directory and proceed with the exercise.
