Difference between revisions of "Tutorials"

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==Tutorials for Courses==
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* [[Tutorials#FastLMM_&_GCTA|FastLMM & GCTA]] 
 +
* [[Tutorials#Mendelian Randomization|Mendelian Randomization]]
 +
* [[Tutorials#Pleiotropy|Pleiotropy]]
 +
* [[Tutorials#PLINK_GWAS:_Data_Quality_Control_and Association_Analysis_Controlling_for_Population_Substructure|PLINK GWAS: QC and Controlling for Population Substructure]]
 +
* [[Tutorials#Power_Analysis|Power Analysis]]
 +
* [[Tutorials#REGENIE|REGENIE]]
 +
* [[Tutorials#Regression_and_Intro_to_PLINK_and_R|Regression and Intro to PLINK and R]]
 +
* [[Tutorials#Pencil_and_Paper_Exercise|Pencil and Paper Exercise]]
 +
 
==Running Tutorials on Your Computer==
 
==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 [https://www.vultr.com/ VULTR]. Second, you can install a Virtual Machine program (such as [https://www.virtualbox.org/ 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 [[VirtualBox Installation|here]] to install VirtualBox on your computer.
+
We adopt [https://www.docker.com/ docker] to run our course material, and we have created various [https://hub.docker.com/u/statisticalgenetics docker repositories] with freely available Docker images for users to readily run our exercises on their own computers using [https://docs.docker.com/desktop/ Docker Desktop]. These docker images are for multi-platform use (Mac, Windows, or Linux). More information regarding instructions to install Docker Desktop and to run the course material on your computer is detailed in the documentation below. 
−
 
+
−
The VM Image is available [https://statgen.research.bcm.edu/files/images/Statgen.ova 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.
+
−
 
+
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<pre>echo "deb [trusted=yes] https://statgen.us/deb ./" | sudo tee -a /etc/apt/sources.list.d/statgen.list
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sudo add-apt-repository -y ppa:webupd8team/java
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sudo apt-get update
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</pre>
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+
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We have made a video tutorial to show you how to install the repository step by step which is available [https://www.youtube.com/watch?v=5jRJHXxkC9g&t=19s here]. If you want to install specific exercise at your demands, please refer to commands listed in each section below.
+
−
 
+
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==Alohomora==
+
−
* [http://statgen.us/files/tutorials/seqspark/Alohomora_Exercise_revised.pdf Exercise <nowiki>[PDF]</nowiki>]
+
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* [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Data Set]
+
−
* [http://gmc.mdc-berlin.de/alohomora/ Software Link]
+
−
 
+
−
==Annotation==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.2019.docx Functional Annotation Exercise <nowiki>[DOCX]</nowiki>]
+
−
* [[Commands in Annotation Exercise|Exercise Commands]]
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>
+
−
statgen-setup login --tutorial annovar
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−
</pre>
+
−
 
+
−
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
+
−
 
+
−
==Annovar MEndelian==
+
−
* [http://statgen.us/files/tutorials/FunctionalAnnotation_Annovar_final.pdf Exercise <nowiki>[PDF]</nowiki>]
+
−
* [https://statgen.research.bcm.edu/files/2017/09/commands/annovar-functional_annotation.txt Commands Part I - Functional Annotation]
+
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* [https://statgen.research.bcm.edu/files/2017/09/commands/annovar-variant_filtering.txt Commands Part II - Variant Filtering]
+
−
 
+
−
==Cochran Armitage Trend Test==
+
−
* [http://statgen.us/files/tutorials/Armitage_sample_size_revised.pdf CATT Exercise <nowiki>[PDF]</nowiki>]
+
−
 
+
−
==GATK and IGV==
+
−
* [http://statgen.us/files/tutorials/Variant_calling_exercices_GATK_IGV.pdf GATK/IGV Exercise <nowiki>[PDF]</nowiki>]
+
−
 
+
−
====Software Links====
+
−
:* [https://www.broadinstitute.org/gatk/ GATK]
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−
:* [http://www.broadinstitute.org/igv/ IGV] ([http://statgen.us/files/software/igv.jar Download JAR file])
+
−
 
+
−
====Result Files====
+
−
:* [http://statgen.us/files/2016/07/gatk_results.tar.gz GATK/IGV exercise]
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−
 
+
−
==Gemini==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Gemini.docx Gemini exercise <nowiki>[DOCX]</nowiki>]
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>
+
−
statgen-setup login --tutorial gemini
+
−
</pre>
+
−
 
+
−
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
+
−
 
+
−
==GenABEL==
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* [http://statgen.us/files/tutorials/genabel/GenABEL_with_PLINK1.9.pdf GenABEL Exercise <nowiki>[PDF]</nowiki>]
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−
* [[GeneABEL Exercise|Exercise Commands]]
+
−
 
+
−
To install from packages, follow the configuration steps above and run the following command.
+
−
 
+
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<pre>sudo apt-get install genabel-tutorial</pre>
+
−
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==
+
−
* [http://statgen.us/files/tutorials/genehunter/Mult_Genehunter.pdf <nowiki>[PDF]</nowiki>]
+
−
* [[Genehunter Exercise|Exercise Commands]]
+
−
 
+
−
 
+
−
To install from packages, follow the configuration steps above and run the following command.
+
−
 
+
−
<pre>sudo apt-get install genehunter-tutorial</pre>
+
−
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==
+
−
* [http://statgen.us/files/tutorials/gwas-qc/PLINK_data_QC_V2.pdf Exercise <nowiki>[PDF]</nowiki>]
+
−
* [[GWAS Data QC Exercise|Exercise Commands]]
+
−
 
+
−
====Installing Packages====
+
−
To install from packages, follow the configuration steps above and run the following command.
+
−
 
+
−
<pre>sudo apt-get install plink-tutorial</pre>
+
−
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==
+
−
* [http://statgen.us/files/tutorials/gwas-substructure/GWAS_Data_Controlling_for_Substructure_V2.pdf Exercise <nowiki>[PDF]</nowiki>]
+
−
* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]
+
−
 
+
−
====Installing Packages====
+
−
To install from packages, follow the configuration steps above and run the following command.
+
−
 
+
−
<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.
+
−
 
+
−
==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==
+
−
* [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>]
+
−
* [http://statgen.us/files/igv_exercise.zip Exercise files (VCF and BAM)]
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>
+
−
statgen-setup login --tutorial igv
+
−
</pre>
+
−
 
+
−
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
+
−
 
+
−
==Linkage/FastLinkage==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/MLINK.pdf LINKAGE Exercise <nowiki>[DOCX]</nowiki>]
+
−
 
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>
+
−
statgen-setup login --tutorial mlink
+
−
</pre>
+
−
 
+
−
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
+
−
 
+
−
<!--
+
−
==Population Genetics==
+
−
* [http://statgen.us/files/tutorials/population/berlinseq.2.2.PopGen_exercise.pdf Population Exercise <nowiki>[PDF]</nowiki>]
+
−
* [http://statgen.us/files/tutorials/population/berlinseq.2.2.PopGen_answers.pdf Exercise Answers <nowiki>[PDF]</nowiki>]
+
−
* [http://statgen.us/files/tutorials/population/popgen_drift.q Commands for popgen_drift]
+
−
* [http://statgen.us/files/tutorials/population/popgen_selection.q Commands for popgen_selection]
+
−
-->
+
−
==Population Genetics==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PopGen.docx Popgen Exercise <nowiki>[DOCX]</nowiki>]
+
−
 
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>
+
−
statgen-setup login --tutorial popgen
+
−
</pre>
+
−
 
+
−
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
+
−
 
+
−
==PSEQ==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PSEQ.doc PSEQ Exercise <nowiki>[DOCX]</nowiki>]
+
−
* [[PSEQ Commands in Exercise|Exercise Commands]]
+
−
 
+
−
To run the exercise from docker image provided,
+
  
−
<pre>
+
===General instructions===
−
statgen-setup login --tutorial pseq
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Statistical_Genetics_Exercise_Instructions.pdf Instructions to install Docker Desktop and running the course material on your computer]
−
</pre>
+
  
−
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
+
===Tutorial specific instructions===
 +
Please refer to the previous section for instructions on the installation of Docker Desktop and basic usages. 
  
−
==Regression==
+
Material and instructions for specific exercise are listed in each section below. They provide links to pdf versions of the exercises and a minimal set of commands to use for downloading the docker images and running an exercise. 
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/regression.docx Regression Exercise <nowiki>[DOCX]</nowiki>]
+
−
* [[Regression_Exercise|Exercise Commands]]
+
  
−
To run the exercise from docker image provided,
+
==FastLMM & GCTA==
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/FastLMM_GCTA.pdf FastLMM & GCTA Exercise [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/FastLMM_GCTA_Outputs.pdf FastLMM & GCTA Output [PDF]]
 +
* [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta FastLMM & GCTA Docker Image]
  
−
<pre>
+
To pull and download the docker image from the Docker Hub repository,
−
statgen-setup login --tutorial regression
+
−
</pre>
+
  
−
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
+
<pre>docker pull statisticalgenetics/fastlmm-gcta</pre>
 +
To run the exercise from the downloaded docker image,
  
−
==RV-TDT==
+
<pre>docker run --rm -p 8888:8888 statisticalgenetics/fastlmm-gcta</pre>
−
* [http://statgen.us/files/tutorials/rvtdt/rvtdt_exercise_v3.pdf Exercise <nowiki>[PDF]</nowiki>]
+
−
* [[RV-TDT|Exercise Commands]]
+
  
−
====Installing Packages====
+
==Mendelian Randomization==
−
To install from packages, follow the configuration steps above and run the following command.
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Mendelian_Randomization.pdf Mendelian Randomization Exercise [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Mendelian_Randomization_Outputs.pdf// Mendelian Randomization Output [PDF]]
 +
* [https://hub.docker.com/r/statisticalgenetics/mendelian-randomization Mendelian Randomization Docker Image]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Mendelian_Randomization_Questions.pdf Mendelian Randomization Questions [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Mendelian_Randomization_Answers.pdf Mendelian Randomization Answers [PDF]]
  
−
<pre>sudo apt-get install rvtdt-tutorial</pre>
+
To pull and download the docker image from the Docker Hub repository,
−
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==
+
<pre>docker pull statisticalgenetics/mendelian-randomization</pre>
−
* [http://statgen.us/files/tutorials/SEQLinkage/SEQLinkage_revised_with_pg_numb.pdf SEQLinkage Exercise <nowiki>[PDF]</nowiki>]
+
To run the exercise from the downloaded docker image,
−
* [[SEQLinkage_Commands_in_Exercise|Exercise Commands]]
+
  
 +
<pre>docker run --rm -p 8888:8888 statisticalgenetics/mendelian-randomization</pre>
  
−
To install from packages, follow the configuration steps above and run the following command.
+
==Pleiotropy and Mediation Analysis==
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Pleiotropy.pdf Pleiotropy Exercise [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Pleiotropy_Outputs.pdf Pleiotropy Output [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy_answers.pdf Pleiotropy Docker Image]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Pleiotropy_Questions.pdf Pleiotropy Questions [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Pleiotropy_Answers.pdf Pleiotropy Answers [PDF]]
  
−
<pre>sudo apt-get install seqlinkage-tutorial</pre>
+
To pull and download the docker image from the Docker Hub repository,
−
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==
+
<pre>docker pull statisticalgenetics/pleiotropy</pre>
−
* [http://statgen.us/files/tutorials/seqspark/SEQSpark_exercise_Final_v4.pdf SEQSpark Exercise <nowiki>[PDF]</nowiki>]
+
To run the exercise from the downloaded docker image,
−
* [[SEQSpark|Exercise Commands]]
+
−
* [http://statgen.us/files/images/SEQSpark.ova Virtual Machine Image]
+
  
−
====Installing Packages====
+
<pre>docker run --rm -p 8888:8888 statisticalgenetics/pleiotropy</pre>
−
To install from packages, follow the configuration steps above and run the following command.
+
  
−
<pre>sudo apt-get install seqspark-tutorial</pre>
+
==PLINK GWAS: Data Quality Control and Association Analysis Controlling for Population Substructure==
−
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
+
These exercises run using a shared docker image, however the exercises are split into two separate notebooks.
−
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==
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_Data_QC.pdf PLINK GWAS: Data QC Exercise [PDF]]
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Slink.doc SLINK Exercise <nowiki>[DOCX]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_Data_QC_Outputs.pdf PLINK GWAS: Data QC Output [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_Data_QC_Questions.pdf PLINK GWAS: Data QC Questions [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_Data_QC_Answers.pdf PLINK GWAS: Data QC Answers [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_GWAS_Substructure.pdf PLINK GWAS: Population Substructure Exercise [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_GWAS_Substructure_Outputs.pdf PLINK GWAS: Population Substructure Output [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_GWAS_Substructure_Questions.pdf PLINK GWAS: Population Substructure Questions [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_GWAS_Substructure_Answers.pdf PLINK GWAS: Population Substructure Answers [PDF]]
 +
* [https://hub.docker.com/r/statisticalgenetics/plink-gwas PLINK GWAS Docker Image]
  
−
To run the exercise from docker image provided,
+
To pull and download the docker image from the Docker Hub repository,
  
−
<pre>
+
<pre>docker pull statisticalgenetics/plink-gwas</pre>
−
statgen-setup login --tutorial slink
+
To run the exercise from the downloaded docker image,
−
</pre>
+
  
−
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
+
<pre>docker run --rm -p 8888:8888 statisticalgenetics/plink-gwas</pre>
  
 +
==Power Analysis==
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Power_Calculations_Questions.pdf Power Analysis Questions [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Power_Calculations_Answers.pdf Power Analysis Answers [PDF]]
  
−
==SUPERLINK==
+
==REGENIE==
−
* [http://statgen.us/files/tutorials/Superlink_Exercise_v2.pdf SUPERLINK Exercise <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regenie.pdf Regenie Exercise [PDF]]
−
* [https://statgen.research.bcm.edu/files/2016/10/data/superlink.zip Superlink]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regenie_Outputs.pdf Regenie Output [PDF]]
 +
* [https://hub.docker.com/r/statisticalgenetics/regenie Regenie Docker Image]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regenie_Questions.pdf Regenie Questions [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regenie_Answers.pdf Regenie Answers [PDF]]
  
−
==Variant Association Tools==
+
To pull and download the docker image from the Docker Hub repository,
−
* [https://statgenetics.github.io/statgen-courses/notebooks/VAT.html VAT Exercise <nowiki>[HTML]</nowiki>]
+
−
* [[VAT Commands in Exercise|Exercise Commands]]
+
  
 +
<pre>docker pull statisticalgenetics/regenie</pre>
 +
To run the exercise from the downloaded docker image,
  
−
To run the exercise from docker image provided,
+
<pre>docker run --rm -p 8888:8888 statisticalgenetics/regenie</pre>
  
−
<pre>
+
==Regression and Intro to PLINK and R==
−
statgen-setup login --tutorial vat
+
These exercises run using a shared docker image, however the exercises are split into two separate notebooks.
−
</pre>
+
  
−
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regression.pdf Regression Exercise [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regression_Outputs.pdf Regression Output [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regression_Questions.pdf Regression Questions [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regression_Answers.pdf Regression Answers [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Intro_Plink_R.pdf Intro to PLINK & R Exercise [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Intro_Plink_R_Outputs.pdf Intro to PLINK & R Output [PDF]]
 +
* [https://hub.docker.com/r/statisticalgenetics/regression-plink-r Regression and Intro to PLINK & R Docker Image]
  
−
==VAT Mendelian==
+
To pull and download the docker image from the Docker Hub repository,
−
* [http://statgen.us/files/tutorials/VAT_Mendelian.pdf Exercise <nowiki>[PDF]</nowiki>]
+
−
* [[VAT mendelian commands|Exercise Commands]]
+
  
 +
<pre>docker pull statisticalgenetics/regression-plink-r</pre>
 +
To run the exercise from the downloaded docker image,
  
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To install from packages, follow the configuration steps above and run the following command.
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<pre>docker run --rm -p 8888:8888 statisticalgenetics/regression-plink-r</pre>
  
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<pre>sudo apt-get install vtools-mendelian-tutorial</pre>
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==Pencil and Paper Exercise==
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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.
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Population_Genetics_Questions.pdf Population Genetics Questions [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Population_Genetics_Answers.pdf Population Genetics Answers [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Linkage_Disequilibrium_Questions.pdf Linkage Disequilibrium Questions [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Linkage_Disequilibrium_Answers.pdf Linkage Disequilibrium Answers [PDF]]

Latest revision as of 10:43, 22 September 2026

Tutorials for Courses

Running Tutorials on Your Computer

We adopt docker to run our course material, and we have created various docker repositories with freely available Docker images for users to readily run our exercises on their own computers using Docker Desktop. These docker images are for multi-platform use (Mac, Windows, or Linux). More information regarding instructions to install Docker Desktop and to run the course material on your computer is detailed in the documentation below. 

General instructions

Tutorial specific instructions

Please refer to the previous section for instructions on the installation of Docker Desktop and basic usages. 

Material and instructions for specific exercise are listed in each section below. They provide links to pdf versions of the exercises and a minimal set of commands to use for downloading the docker images and running an exercise. 

FastLMM & GCTA

To pull and download the docker image from the Docker Hub repository, 

docker pull statisticalgenetics/fastlmm-gcta

To run the exercise from the downloaded docker image, 

docker run --rm -p 8888:8888 statisticalgenetics/fastlmm-gcta

Mendelian Randomization

To pull and download the docker image from the Docker Hub repository, 

docker pull statisticalgenetics/mendelian-randomization

To run the exercise from the downloaded docker image, 

docker run --rm -p 8888:8888 statisticalgenetics/mendelian-randomization

Pleiotropy and Mediation Analysis

To pull and download the docker image from the Docker Hub repository, 

docker pull statisticalgenetics/pleiotropy

To run the exercise from the downloaded docker image, 

docker run --rm -p 8888:8888 statisticalgenetics/pleiotropy

PLINK GWAS: Data Quality Control and Association Analysis Controlling for Population Substructure

These exercises run using a shared docker image, however the exercises are split into two separate notebooks.

To pull and download the docker image from the Docker Hub repository, 

docker pull statisticalgenetics/plink-gwas

To run the exercise from the downloaded docker image, 

docker run --rm -p 8888:8888 statisticalgenetics/plink-gwas

Power Analysis

REGENIE

To pull and download the docker image from the Docker Hub repository, 

docker pull statisticalgenetics/regenie

To run the exercise from the downloaded docker image, 

docker run --rm -p 8888:8888 statisticalgenetics/regenie

Regression and Intro to PLINK and R

These exercises run using a shared docker image, however the exercises are split into two separate notebooks.

To pull and download the docker image from the Docker Hub repository, 

docker pull statisticalgenetics/regression-plink-r

To run the exercise from the downloaded docker image, 

docker run --rm -p 8888:8888 statisticalgenetics/regression-plink-r

Pencil and Paper Exercise

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