Difference between revisions of "Tutorials"
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==IGV== | ==IGV== | ||
| − | * [ | + | * [http://statgen.us/files/software/igv/igv-2.3.97.jar igv.jar Software Link] |
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/IGV.docx IGV exercise <nowiki>[DOCX]</nowiki>] | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/IGV.docx IGV exercise <nowiki>[DOCX]</nowiki>] | ||
| + | * [http://statgen.us/files/igv_exercise.zip Exercise files (VCF and BAM)] | ||
To run the exercise from docker image provided, | To run the exercise from docker image provided, | ||
Revision as of 15:07, 21 November 2019
Contents
- 1 Running Tutorials on Your Computer
- 2 Alohomora
- 3 Annotation
- 4 Annovar MEndelian
- 5 Cochran Armitage Trend Test
- 6 GATK and IGV
- 7 Gemini
- 8 GenABEL
- 9 Genehunter
- 10 GWAS: Data Quality Control
- 11 GWAS: Association Analysis Controlling for Population Substructure
- 12 Homozygosity Mapper
- 13 IGV
- 14 Linkage/FastLinkage
- 15 Population Genetics
- 16 PSEQ
- 17 Regression
- 18 RV-TDT
- 19 SEQLinkage
- 20 SEQSpark
- 21 SLINK
- 22 SUPERLINK
- 23 Variant Association Tools
- 24 VAT Mendelian
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. You can refer to these online videos here to install VirtualBox on your computer.
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.us/deb ./" | sudo tee -a /etc/apt/sources.list.d/statgen.list sudo add-apt-repository -y ppa:webupd8team/java sudo apt-get update
We have made a video tutorial to show you how to install the repository step by step which is available here. If you want to install specific exercise at your demands, please refer to commands listed in each section below.
Alohomora
Annotation
To run the exercise from docker image provided,
statgen-setup login --tutorial annovar
The "statgen-setup" script is available here and can be installed following these instructions.
Annovar MEndelian
Cochran Armitage Trend Test
GATK and IGV
Software Links
Result Files
Gemini
To run the exercise from docker image provided,
statgen-setup login --tutorial gemini
The "statgen-setup" script is available here and can be installed following these instructions.
GenABEL
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install genabel-tutorial
The exercise's files will then be installed in the folder /home/shared/genabel. You can run from there or copy the files into your user's home directory and proceed with the exercise.
Genehunter
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install genehunter-tutorial
The exercise's files will then be installed in the folder /home/shared/genehunter. You can run from there or copy the files into your user's home directory and proceed with the exercise.
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.
Homozygosity Mapper
IGV
To run the exercise from docker image provided,
statgen-setup login --tutorial igv
The "statgen-setup" script is available here and can be installed following these instructions.
Linkage/FastLinkage
To run the exercise from docker image provided,
statgen-setup login --tutorial mlink
The "statgen-setup" script is available here and can be installed following these instructions.
Population Genetics
To run the exercise from docker image provided,
statgen-setup login --tutorial popgen
The "statgen-setup" script is available here and can be installed following these instructions.
PSEQ
To run the exercise from docker image provided,
statgen-setup login --tutorial pseq
The "statgen-setup" script is available here and can be installed following these instructions.
Regression
To run the exercise from docker image provided,
statgen-setup login --tutorial regression
The "statgen-setup" script is available here and can be installed following these instructions.
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.
SEQLinkage
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install seqlinkage-tutorial
The exercise's files will then be installed in the folder /home/shared/seqlinkage. You can run from there or copy the files into your user's home directory and proceed with the exercise.
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.
SLINK
To run the exercise from docker image provided,
statgen-setup login --tutorial slink
The "statgen-setup" script is available here and can be installed following these instructions.
SUPERLINK
Variant Association Tools
To run the exercise from docker image provided,
statgen-setup login --tutorial vat
The "statgen-setup" script is available here and can be installed following these instructions.
VAT Mendelian
To install from packages, follow the configuration steps above and run the following command.
sudo apt-get install vtools-mendelian-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.
