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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) 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. 
  
−
In this document we will focus on discussing how to set it up and run course tutorials on your computer, using these docker images and optionally a utility script we created to streamline various docker commands.
+
===General instructions===
−
 
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* [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]
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===Pre-requisites===
+
−
Software you need to install on your computer are <code>SoS</code> (a workflow system to run our course utility script) and <code>docker</code>.
+
−
 
+
−
====Mac and Linux users====
+
−
<code>SoS</code> requires Python 3.6+ to run. It is recommended that you install [https://docs.conda.io/en/latest/miniconda.html Miniconda] to run Python 3 if you don't have it already. Once you have Python 3 installed, simply type <code>pip install sos</code> to install <code>SoS</code>, or, check out [https://vatlab.github.io/sos-docs/running.html here for alternative installation methods] if you have troubles with that command. To install <code>docker</code> from command line please follow our instructions [http://statgen.us/lab-wiki/orientation/jupyter-setup.html#install-docker here]. Alternatively Mac users can download docker app for Mac and install from a graphical interface.
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−
 
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Finally please download our utility script [https://raw.githubusercontent.com/statgenetics/statgen-courses/master/src/statgen-setup <code>src/statgen-setup</code>] to your <code>PATH</code> and change it to executable, eg, <code>chmod +x ~/bin/statgen-setup</code> if you put it under <code>~/bin</code> which is part of your <code>PATH</code>. To verify your setup, type:
+
−
 
+
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<pre>statgen-setup -h</pre>
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you should see some meaningful output.
+
−
 
+
−
====Windows users====
+
−
Running these tutorials in Windows is currently not supported. Although in principle these docker images will also work in Windows, this has not yet been tested out and we are unable to provide sure instructions to setting it up. The utility script "statgen-setup" that we provide will certainly need adjustments (though minor) to work with Windows.
+
  
 
===Tutorial specific instructions===
 
===Tutorial specific instructions===
−
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. For advanced options and other features provided by our utility script please read here our [https://github.com/statgenetics/statgen-courses/blob/master/README.md complete documentation to the utility script].
+
Please refer to the previous section for instructions on the installation of Docker Desktop and basic usages. 
−
 
+
−
==Alohomora==
+
−
* [http://statgen.us/files/tutorials/seqspark/Alohomora_Exercise_revised.pdf Exercise <nowiki>[PDF]</nowiki>]
+
−
* [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Data Set]
+
−
* [http://gmc.mdc-berlin.de/alohomora/ Software Link]
+
−
 
+
−
==Annotation==
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−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.docx Functional Annotation Exercise <nowiki>[DOCX]</nowiki>]
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* [[Commands in Annotation Exercise|Exercise Commands]]
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
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<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==
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−
* [http://statgen.us/files/tutorials/FunctionalAnnotation_Annovar_final.pdf Exercise <nowiki>[PDF]</nowiki>]
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−
* [https://statgen.research.bcm.edu/files/2017/09/commands/annovar-functional_annotation.txt Commands Part I - Functional Annotation]
+
−
* [https://statgen.research.bcm.edu/files/2017/09/commands/annovar-variant_filtering.txt Commands Part II - Variant Filtering]
+
−
 
+
−
==Cochran Armitage Trend Test==
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−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Armitage_sample_size.pdf CATT Exercise <nowiki>[PDF]</nowiki>]
+
−
 
+
−
==FastLMM==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FASTLMM.pdf FastLMM exercise <nowiki>[PDF]</nowiki>]
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−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
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<pre>statgen-setup login --tutorial fastlmm-gcta
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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].
+
−
 
+
−
==GCTA==
+
−
 
+
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* [https://github.com/statgenetics/statgen-courses/blob/master/handout/GCTA.pdf GCTA exercise <nowiki>[PDF]</nowiki>]
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−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup login --tutorial fastlmm-gcta
+
−
</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].
+
−
 
+
−
==Gemini==
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* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Gemini.docx Gemini exercise <nowiki>[DOCX]</nowiki>]
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−
 
+
−
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].
+
−
 
+
−
 
+
−
==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.docx Exercise <nowiki>[PDF]</nowiki>]
+
−
* [[GWAS Data QC Exercise|Exercise Commands]]
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup login --tutorial plink
+
−
</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].
+
−
 
+
−
 
+
−
==GWAS: Association Analysis Controlling for Population Substructure==
+
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_Substructure.docx Exercise <nowiki>[PDF]</nowiki>]
+
−
* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]
+
−
 
+
−
To run the exercise from docker image provided,
+
−
 
+
−
<pre>statgen-setup login --tutorial plink
+
−
</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].
+
−
 
+
−
 
+
−
==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)]
+
−
 
+
−
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,
+
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. 
  
−
<pre>statgen-setup login --tutorial pseq
+
==FastLMM & GCTA==
−
</pre>
+
* [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]
  
−
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].
+
To pull and download the docker image from the Docker Hub repository,
  
−
==Regression==
+
<pre>docker pull statisticalgenetics/fastlmm-gcta</pre>
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/regression.docx Regression Exercise <nowiki>[DOCX]</nowiki>]
+
To run the exercise from the downloaded docker image,
−
* [[Regression_Exercise|Exercise Commands]]
+
  
−
To run the exercise from docker image provided,
+
<pre>docker run --rm -p 8888:8888 statisticalgenetics/fastlmm-gcta</pre>
  
−
<pre>statgen-setup login --tutorial regression
+
==Mendelian Randomization==
−
</pre>
+
* [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]]
  
−
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].
+
To pull and download the docker image from the Docker Hub repository,
  
−
==RV-TDT==
+
<pre>docker pull statisticalgenetics/mendelian-randomization</pre>
−
* [http://statgen.us/files/tutorials/rvtdt/rvtdt_exercise_v3.pdf Exercise <nowiki>[PDF]</nowiki>]
+
To run the exercise from the downloaded docker image,
−
* [[RV-TDT|Exercise Commands]]
+
  
−
====Installing Packages====
+
<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.
+
  
−
<pre>sudo apt-get install rvtdt-tutorial</pre>
+
==Pleiotropy and Mediation Analysis==
−
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.
+
* [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]]
  
−
==SEQLinkage==
+
To pull and download the docker image from the Docker Hub repository,
−
* [http://statgen.us/files/tutorials/SEQLinkage/SEQLinkage_revised_with_pg_numb.pdf SEQLinkage Exercise <nowiki>[PDF]</nowiki>]
+
−
* [[SEQLinkage_Commands_in_Exercise|Exercise Commands]]
+
  
 +
<pre>docker pull statisticalgenetics/pleiotropy</pre>
 +
To run the exercise from the downloaded docker image,
  
−
To install from packages, follow the configuration steps above and run the following command.
+
<pre>docker run --rm -p 8888:8888 statisticalgenetics/pleiotropy</pre>
  
−
<pre>sudo apt-get install seqlinkage-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/seqlinkage''. You can run from there or copy the files into your user's home directory and proceed with the exercise.
+
These exercises run using a shared docker image, however the exercises are split into two separate notebooks.
  
−
==SEQSpark==
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_Data_QC.pdf PLINK GWAS: Data QC Exercise [PDF]]
−
* [http://statgen.us/files/tutorials/seqspark/SEQSpark_exercise_Final_v4.pdf SEQSpark Exercise <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_Data_QC_Outputs.pdf PLINK GWAS: Data QC Output [PDF]]
−
* [[SEQSpark|Exercise Commands]]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_Data_QC_Questions.pdf PLINK GWAS: Data QC Questions [PDF]]
−
* [http://statgen.us/files/images/SEQSpark.ova Virtual Machine Image]
+
* [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]
  
−
====Installing Packages====
+
To pull and download the docker image from the Docker Hub repository,
−
To install from packages, follow the configuration steps above and run the following command.
+
  
−
<pre>sudo apt-get install seqspark-tutorial</pre>
+
<pre>docker pull statisticalgenetics/plink-gwas</pre>
−
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
+
To run the exercise from the downloaded docker image,
−
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==
+
<pre>docker run --rm -p 8888:8888 statisticalgenetics/plink-gwas</pre>
−
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Slink.doc SLINK Exercise <nowiki>[DOCX]</nowiki>]
+
  
−
To run the exercise from docker image provided,
+
==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]]
  
−
<pre>statgen-setup login --tutorial slink
+
==REGENIE==
−
</pre>
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regenie.pdf Regenie Exercise [PDF]]
 +
* [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]]
  
−
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].
+
To pull and download the docker image from the Docker Hub repository,
  
 +
<pre>docker pull statisticalgenetics/regenie</pre>
 +
To run the exercise from the downloaded docker image,
  
 +
<pre>docker run --rm -p 8888:8888 statisticalgenetics/regenie</pre>
  
−
==SUPERLINK==
+
==Regression and Intro to PLINK and R==
−
* [http://statgen.us/files/tutorials/Superlink_Exercise_v2.pdf SUPERLINK Exercise <nowiki>[PDF]</nowiki>]
+
These exercises run using a shared docker image, however the exercises are split into two separate notebooks.
−
* [https://statgen.research.bcm.edu/files/2016/10/data/superlink.zip Superlink]
+
  
−
==Variant Association Tools==
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regression.pdf Regression Exercise [PDF]]
−
* [https://statgenetics.github.io/statgen-courses/notebooks/VAT.html VAT Exercise <nowiki>[HTML]</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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* [[VAT Commands in Exercise|Exercise Commands]]
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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]]
 +
* [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,
  
−
To run the exercise from docker image provided,
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<pre>docker pull statisticalgenetics/regression-plink-r</pre>
 +
To run the exercise from the downloaded docker image,
  
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<pre>statgen-setup login --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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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].
+
==Pencil and Paper 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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