Difference between revisions of "Tutorials"

From Center for Statistical Genetics

Jump to: navigation, search
Line 46: Line 46:
 
====Result Files====
 
====Result Files====
 
:* [http://statgen.us/files/2016/07/gatk_results.tar.gz GATK/IGV exercise]
 
:* [http://statgen.us/files/2016/07/gatk_results.tar.gz GATK/IGV exercise]
 +
 +
==Gemini==
 +
* [https://drive.google.com/file/d/0B2pJ9cgevF3sTS1DeGxYalFTN00/view Bam files for exercise]
  
 
==GenABEL==
 
==GenABEL==
Line 79: Line 82:
 
<pre>sudo apt-get install plink-tutorial</pre>
 
<pre>sudo apt-get install plink-tutorial</pre>
 
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.
 
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==
 +
*[http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_1.pdf Exercise Part I]
 +
*[http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_2.pdf Exercise Part II]
 +
*[http://www.homozygositymapper.org Data Sets]
 +
 +
==IGV==
 +
*[https://statgen.research.bcm.edu/files/software/igv/igv-2.3.97.jar igv.jar Software Link]
 +
*[https://statgen.research.bcm.edu/files/2017/09/data/igv_exercise.zip BAM and VCF Files]
  
 
==Linkage/FastLinkage==
 
==Linkage/FastLinkage==

Revision as of 11:15, 15 June 2018

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.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.

 

Alohorma

Annotation

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

sudo apt-get install annotation-tutorial

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

Annovar MEndelian

Cochran Armitage Trend Test

GATK and IGV

Software Links

Result Files

Gemini

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

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

Linkage/FastLinkage

Population Genetics

PSEQ

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

sudo apt-get install plinkseq-tutorial

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

Regression

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

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

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

SUPERLINK

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.

VAT Mendelian