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==Tutorials for Courses==
 +
* [[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==
−
Starting Fall 2019 we adopt [https://www.docker.com/ docker] to run our course material . We have created various [https://hub.docker.com/u/statisticalgenetics docker repositories] with source material freely available from [https://github.com/statgenetics/statgen-courses github] for users to readily setup and reproduce our tutorials on their own computers. These docker images can also be used as production tool to run relevant software on your computer (Mac, Linux or Windows) or even a high performance computing cluster (if properly configured) for your own data analysis.
+
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. 
  
 
===General instructions===
 
===General instructions===
−
* [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#alternative-to-cloud-server-use-your-own-computer Instructions to setup course tutorial environment on your computer]
+
* [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]
−
* [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#option-1-launch-exercise-in-jupyterlab Instructions to run course tutorial through JupyterLab]
+
−
* [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#option-2-launch-from-command-shell Instructions to run course tutorial through command line terminal]
+
−
 
+
  
 
===Tutorial specific instructions===
 
===Tutorial specific instructions===
−
We use a script [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup "statgen-setup"] to start the docker based environments for these tutorials. Please refer to the previous section for instructions on the installation of this script.
+
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 (''only those using statgen-setup command are relevant to our docker based tutorials''). They provide links to materials and a minimal set of commands to use for launching and running an exercise. Command "statgen-setup login" will allow you to start and login to a Linux command line environment (regardless of your current computational environment) to perform all analysis in command shells. This works for all the tutorials on this page. Additionally, some tutorials support command "statgen-setup launch" which will start a JupyterLab server to perform the analysis.
+
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. 
  
−
==Alohomora==
+
==FastLMM & GCTA==
−
* [http://statgen.us/files/tutorials/seqspark/Alohomora_Exercise_revised.pdf Exercise <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/FastLMM_GCTA.pdf FastLMM & GCTA Exercise [PDF]]
−
* [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Data Set]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/FastLMM_GCTA_Outputs.pdf FastLMM & GCTA Output [PDF]]
−
* [http://gmc.mdc-berlin.de/alohomora/ Software Link]
+
* [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta FastLMM & GCTA Docker Image]
  
−
==Annovar complex traits==
+
To pull and download the docker image from the Docker Hub repository,
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.pdf Functional Annotation Exercise <nowiki>[PDF]</nowiki>]
+
−
* [[Commands in Annotation Exercise|Exercise Commands]]
+
  
−
To run the exercise from docker image provided,
+
<pre>docker pull statisticalgenetics/fastlmm-gcta</pre>
 +
To run the exercise from the downloaded docker image,
  
−
<pre>statgen-setup login --tutorial annovar
+
<pre>docker run --rm -p 8888:8888 statisticalgenetics/fastlmm-gcta</pre>
−
</pre>
+
  
−
==Annovar Mendelian traits==
+
==Mendelian Randomization==
−
* [http://statgen.us/files/tutorials/FunctionalAnnotation_Annovar_final.pdf Exercise <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Mendelian_Randomization.pdf Mendelian Randomization Exercise [PDF]]
−
* [https://statgen.us/files/2017/09/commands/annovar-functional_annotation.txt Commands Part I - Functional Annotation]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Mendelian_Randomization_Outputs.pdf// Mendelian Randomization Output [PDF]]
−
* [https://statgen.us/files/2017/09/commands/annovar-variant_filtering.txt Commands Part II - Variant Filtering]
+
* [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]]
  
−
==Cochran Armitage Trend Test==
+
To pull and download the docker image from the Docker Hub repository,
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Armitage_sample_size.pdf CATT Exercise <nowiki>[PDF]</nowiki>]
+
  
 +
<pre>docker pull statisticalgenetics/mendelian-randomization</pre>
 +
To run the exercise from the downloaded docker image,
  
−
 
+
<pre>docker run --rm -p 8888:8888 statisticalgenetics/mendelian-randomization</pre>
−
==Epistasis (PLINK and CASSI)==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Epistasis_PLINK_CASSI.pdf Epistasis exercise <nowiki>[PDF]</nowiki>]
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup login --tutorial epistasis
+
−
</pre>
+
−
 
+
−
 
+
−
==FastLMM==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FASTLMM.pdf FastLMM exercise <nowiki>[PDF]</nowiki>]
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup login --tutorial fastlmm-gcta
+
−
</pre>
+
−
 
+
−
 
+
−
==Fine-mapping (SuSiE method)==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/finemapping.docx susieR Exercise <nowiki>[DOCX]</nowiki>]
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/finemapping_answers.docx susieR Exercise Answers <nowiki>[DOCX]</nowiki>]
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/finemapping.ipynb susieR Exercise <nowiki>[Ipython notebook]</nowiki>]
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/finemapping_answers.ipynb susieR Exercise Answers <nowiki>[Ipython notebook]</nowiki>]
+
−
 
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup launch --tutorial finemap
+
−
</pre>
+
−
 
+
−
==GCTA==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/GCTA.pdf GCTA exercise <nowiki>[PDF]</nowiki>]
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup login --tutorial fastlmm-gcta
+
−
</pre>
+
−
 
+
−
 
+
−
==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>
+
−
 
+
−
 
+
−
==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==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_data_QC.pdf Exercise <nowiki>[PDF]</nowiki>]
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PLINK_Data_QC.ipynb Exercise <nowiki>[IPython Notebook]</nowiki>]
+
−
* [[GWAS Data QC Exercise|Exercise Commands]]
+
−
 
+
−
To run the exercise via JupyterLab from docker image provided,
+
−
 
+
−
<pre>statgen-setup launch --tutorial plink
+
−
</pre>
+
−
 
+
−
Alternatively, you can opt to run the exercise via command terminal from docker image provided,
+
−
 
+
−
<pre>statgen-setup login --tutorial plink
+
−
</pre>
+
−
 
+
−
==GWAS: Association Analysis Controlling for Population Substructure==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_Substructure.pdf Exercise <nowiki>[PDF]</nowiki>]
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PLINK_Substructure.ipynb Exercise <nowiki>[IPython Notebook]</nowiki>]
+
−
* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]
+
−
 
+
−
To run the exercise via JupyterLab from docker image provided,
+
−
 
+
−
<pre>statgen-setup launch --tutorial plink
+
−
</pre>
+
−
 
+
−
Alternatively, you can opt to run the exercise via command terminal from docker image provided,
+
−
 
+
−
<pre>statgen-setup login --tutorial plink
+
−
</pre>
+
−
 
+
−
==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://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)]
+
−
 
+
−
 
+
−
 
+
−
==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>
+
−
 
+
−
==LD clumping==
+
−
* [https://github.com/cumc/bioworkflows/blob/master/GWAS/LD_Clumping.ipynb LD Clumping Exercise <nowiki>[IPython Notebook]</nowiki>]
+
−
 
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup launch --tutorial clumping
+
−
</pre>
+
−
 
+
−
==MR-JTI for TWAS==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/MR_JTI.ipynb MR-JTI Exercise <nowiki>[IPython Notebook]</nowiki>] '''Under Development'''
+
−
 
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup login --tutorial twas
+
−
</pre>
+
  
 
==Pleiotropy==
 
==Pleiotropy==
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy.pdf Pleiotropy Exercise <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Pleiotropy.pdf Pleiotropy Exercise [PDF]]
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy_answers.pdf Pleiotropy Answers to Questions <nowiki>[PDF]</nowiki>]
+
* [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]]
  
−
To run the exercise from docker image provided,
+
To pull and download the docker image from the Docker Hub repository,
  
−
<pre>statgen-setup login --tutorial pleiotropy
+
<pre>docker pull statisticalgenetics/pleiotropy</pre>
−
</pre>
+
To run the exercise from the downloaded docker image,
  
 +
<pre>docker run --rm -p 8888:8888 statisticalgenetics/pleiotropy</pre>
  
−
==Polygenic risk prediction (NPS method)==
+
==PLINK GWAS: Data Quality Control and Association Analysis Controlling for Population Substructure==
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/NPS.pdf PRS NPS Exercise <nowiki>[DOCX]</nowiki>]
+
These exercises run using a shared docker image, however the exercises are split into two separate notebooks.
  
−
To run the exercise from docker image provided,
+
* [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/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]
  
−
<pre>statgen-setup login --tutorial nps
+
To pull and download the docker image from the Docker Hub repository,
−
</pre>
+
  
 +
<pre>docker pull statisticalgenetics/plink-gwas</pre>
 +
To run the exercise from the downloaded docker image,
  
−
==Polygenic risk prediction (LDpred2 method)==
+
<pre>docker run --rm -p 8888:8888 statisticalgenetics/plink-gwas</pre>
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/ldpred2_example.pdf PRS LDpred2 Exercise <nowiki>[PDF]</nowiki>]
+
−
* [https://github.com/cumc/bioworkflows/blob/master/ldpred/ldpred2_example.ipynb PRS LDpred2 Exercise <nowiki>[Ipython Notebook]</nowiki>]
+
  
−
 
+
==Power Analysis==
−
To run the exercise from docker image provided,
+
* [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]]
−
<pre>statgen-setup launch --tutorial ldpred2
+
−
</pre>
+
−
 
+
−
Then follow prompts on the terminal output to open up the JupyterLab server in your web browser. If it is the first time you start this server, please open a command terminal inside JupyterLab, and type
+
−
 
+
−
<pre>get-data</pre>
+
−
 
+
−
to load the data-set to the JupyterLab workspace.
+
−
 
+
−
 
+
−
<!--
+
−
==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>
+
−
 
+
−
 
+
−
==PSEQ==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PSEQ.pdf PSEQ Exercise <nowiki>[PDF]</nowiki>]
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PSEQ.ipynb PSEQ Exercise <nowiki>[Ipython Notebook]</nowiki>]
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup launch --tutorial pseq
+
−
</pre>
+
−
 
+
−
Notice that since PSEQ exercise does not involve generating and visualizing plots, it is also fine to use a command terminal, instead of the JupyterLab server, to run this exercise and reproduce exactly what was described in the tutorial. To do so,
+
−
 
+
−
<pre>statgen-setup login --tutorial pseq
+
−
</pre>
+
  
 
==REGENIE==
 
==REGENIE==
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/regenie_example.pdf REGENIE Exercise <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regenie.pdf Regenie Exercise [PDF]]
−
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/regenie_example.ipynb REGENIE Exercise <nowiki>[Ipython Notebook]</nowiki>]
+
* [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]]
−
To run the exercise from docker image provided,
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regenie_Answers.pdf Regenie Answers [PDF]]
−
 
+
−
<pre>statgen-setup launch --tutorial regenie
+
−
</pre>
+
−
 
+
−
Then follow prompts on the terminal output to open up the JupyterLab server in your web browser. If it is the first time you start this server, please open a command terminal inside JupyterLab, and type
+
−
 
+
−
<pre>get-data</pre>
+
−
 
+
−
to load the data-set to the JupyterLab workspace.
+
−
 
+
−
 
+
−
 
+
−
==Regression==
+
−
* [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,
+
−
 
+
−
<pre>statgen-setup login --tutorial regression
+
−
</pre>
+
−
 
+
−
 
+
−
==RV-TDT==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/RV-TDT.doc Exercise <nowiki>[DOC]</nowiki>]
+
−
* [[RV-TDT|Exercise Commands]]
+
−
 
+
−
====Installing Packages====
+
−
To install from packages, follow the configuration steps above and run the following command.
+
−
 
+
−
<pre>sudo apt-get install rvtdt-tutorial</pre>
+
−
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==
+
−
* [http://statgen.us/files/tutorials/SEQLinkage/SEQLinkage_revised_with_pg_numb.pdf SEQLinkage Exercise <nowiki>[PDF]</nowiki>]
+
−
* [[SEQLinkage_Commands_in_Exercise|Exercise Commands]]
+
−
 
+
−
 
+
−
To install from packages, follow the configuration steps above and run the following command.
+
−
 
+
−
<pre>sudo apt-get install seqlinkage-tutorial</pre>
+
−
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==
+
−
* [http://statgen.us/files/tutorials/seqspark/SEQSpark_exercise_Final_v4.pdf SEQSpark Exercise <nowiki>[PDF]</nowiki>]
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* [[SEQSpark|Exercise Commands]]
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* [http://statgen.us/files/images/SEQSpark.ova Virtual Machine Image]
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====Installing Packages====
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To install from packages, follow the configuration steps above and run the following command.
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<pre>sudo apt-get install seqspark-tutorial</pre>
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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
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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.
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==SLINK==
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To pull and download the docker image from the Docker Hub repository,
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* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Slink.doc SLINK Exercise <nowiki>[DOCX]</nowiki>]
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To run the exercise from docker image provided,
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<pre>docker pull statisticalgenetics/regenie</pre>
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To run the exercise from the downloaded docker image,
  
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<pre>statgen-setup login --tutorial slink</pre>
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<pre>docker run --rm -p 8888:8888 statisticalgenetics/regenie</pre>
  
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==SUPERLINK==
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==Regression and Intro to PLINK and R==
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* [http://statgen.us/files/tutorials/Superlink_Exercise_v2.pdf SUPERLINK Exercise <nowiki>[PDF]</nowiki>]
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These exercises run using a shared docker image, however the exercises are split into two separate notebooks.
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* [https://statgen.research.bcm.edu/files/2016/10/data/superlink.zip Superlink]
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==Variant Association Tools==
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regression.pdf Regression Exercise [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handout/VAT.docx VAT Exercise <nowiki>[DOCX]</nowiki>]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regression_Outputs.pdf Regression Output [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/VAT.ipynb VAT Exercise <nowiki>[Ipython notebook]</nowiki>]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regression_Questions.pdf Regression Questions [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regression_Answers.pdf Regression Answers [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Intro_Plink_R.pdf Intro to PLINK & R Exercise [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Intro_Plink_R_Outputs.pdf Intro to PLINK & R Output [PDF]]
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* [https://hub.docker.com/r/statisticalgenetics/regression-plink-r Regression and Intro to PLINK & R Docker Image]
  
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To pull and download the docker image from the Docker Hub repository,
  
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To run the exercise from docker image provided,
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<pre>docker pull statisticalgenetics/regression-plink-r</pre>
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To run the exercise from the downloaded docker image,
  
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<pre>statgen-setup launch --tutorial vat
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<pre>docker run --rm -p 8888:8888 statisticalgenetics/regression-plink-r</pre>
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</pre>
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Then follow the prompts on the terminal output to open up the JupyterLab server in your web browser. You should find the exercise notebook in the side panel, and you can click to open it.
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==Pencil and Paper Exercise==
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Population_Genetics_Questions.pdf Population Genetics Questions [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Population_Genetics_Answers.pdf Population Genetics Answers [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Linkage_Disequilibrium_Questions.pdf Linkage Disequilibrium Questions [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Linkage_Disequilibrium_Answers.pdf Linkage Disequilibrium Answers [PDF]]

Revision as of 14:58, 10 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

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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