Tutorials

Running Tutorials on Your Computer

We have created a debian repository to make it easier to use our tutorials. This repository allows you to install all required software and example data included in tutorials on your computer. Using this repository will require that you have administrator access to a 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 -y ppa:webupd8team/java
sudo apt-get update

Using the following command you can install all exercises on your computer. If you want to install specific exercise at your demands, please refer to commands listed in each section below.

Annotation

• Functional Annotation Exercise [PDF]
• Commands in Exercise

Cochran Armitage Trend Test

• CATT Exercise [PDF]

GATK and IGV

• GATK/IGV Exercise [PDF]

Software Links

• GATK
• IGV (Download JAR file)

Result Files

• GATK/IGV exercise

GenABEL

• GenABEL Exercise [PDF]
• Commands in Exercise

GWAS: Data Quality Control

• Exercise [PDF]
• Commands in Exercise

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

• Exercise [PDF]
• Commands in Exercise

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.

Population Genetics

• Population Exercise [PDF]
• Exercise Answers [PDF]
• Commands in Exercise

Regression

• Regression Exercise [PDF]
• Commands in Exercise

To install from packages, follow the configuration steps above and run the following command.

sudo apt-get install regression-tutorial

The exercise's files will then be installed in the folder /home/shared/regression. You can run from there or copy the files into your user's home directory and proceed with the exercise.

RV-TDT

• Exercise [PDF]
• Commands in Exercise

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

• Popgen Exercise [PDF]
• Commands for popgen_drift
• Commands for popgen_selection

PSEQ

• PSEQ Exercise [PDF]
• Commands in Exercise

SEQSpark

• SEQSpark Exercise [PDF]
• Commands in Exercise
• Virtual Machine Image

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

• VAT Exercise [PDF]
• Commands in Exercise

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.