Difference between revisions of "Tutorials"

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==Tutorials for Courses==
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* [[Tutorials#FastLMM_&_GCTA|FastLMM & GCTA]] 
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* [[Tutorials#Mendelian Randomization|Mendelian Randomization]]
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* [[Tutorials#Pleiotropy|Pleiotropy]]
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* [[Tutorials#PLINK_GWAS:_Data_Quality_Control_and Association_Analysis_Controlling_for_Population_Substructure|PLINK GWAS: QC and Controlling for Population Substructure]]
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* [[Tutorials#Power_Analysis|Power Analysis]]
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* [[Tutorials#REGENIE|REGENIE]]
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* [[Tutorials#Regression_and_Intro_to_PLINK_and_R|Regression and Intro to PLINK and R]]
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* [[Tutorials#Pencil_and_Paper_Exercise|Pencil and Paper Exercise]]
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==Running Tutorials on Your Computer==
 
==Running Tutorials on Your Computer==
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We have created a debian repository to make it easier to use our tutorials. Using this repository will require that you have administrator access to the computer on which you'll be using them. If you don't have this level of access, we also provide a pre-configured virtual machine image that will allow you to install software as root.
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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. 
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===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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===Tutorial specific instructions===
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Please refer to the previous section for instructions on the installation of Docker Desktop and basic usages. 
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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. 
  
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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.
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==FastLMM & GCTA==
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/FastLMM_GCTA.pdf FastLMM & GCTA Exercise [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/FastLMM_GCTA_Outputs.pdf FastLMM & GCTA Output [PDF]]
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* [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta FastLMM & GCTA Docker Image]
  
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If you would like to use our repository on a VM or on your computer, follow these configuration steps. Please run as the root user or using the sudo command.
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To pull and download the docker image from the Docker Hub repository,
  
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<pre>echo "deb [trusted=yes] https://statgen.research.bcm.edu/deb ./" | sudo tee -a /etc/apt/sources.list.d/statgen.list
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<pre>docker pull statisticalgenetics/fastlmm-gcta</pre>
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sudo add-apt-repository ppa:webupd8team/java
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To run the exercise from the downloaded docker image,
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sudo apt-get update
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</pre>
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==Annotation==
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<pre>docker run --rm -p 8888:8888 statisticalgenetics/fastlmm-gcta</pre>
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[http://statgen.us/files/tutorials/functional-annotation/FunctionalAnnotation_exercise_2018v2.pdf Functional Annotation Exercise <nowiki>[PDF]</nowiki>]
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==GenABEL==
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==Mendelian Randomization==
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[http://statgen.us/files/tutorials/genabel/GenABEL_with_PLINK1.9.pdf GenABEL Exercise <nowiki>[PDF]</nowiki>]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Mendelian_Randomization.pdf Mendelian Randomization Exercise [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Mendelian_Randomization_Outputs.pdf// Mendelian Randomization Output [PDF]]
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* [https://hub.docker.com/r/statisticalgenetics/mendelian-randomization Mendelian Randomization Docker Image]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Mendelian_Randomization_Questions.pdf Mendelian Randomization Questions [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Mendelian_Randomization_Answers.pdf Mendelian Randomization Answers [PDF]]
  
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==GWAS: Data Quality Control==
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To pull and download the docker image from the Docker Hub repository,
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* [http://statgen.us/files/tutorials/gwas-qc/PLINK_data_QC.pdf Exercise <nowiki>[PDF]</nowiki>]
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====Installing Packages====
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<pre>docker pull statisticalgenetics/mendelian-randomization</pre>
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To install from packages, follow the configuration steps above and run the following command.
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To run the exercise from the downloaded docker image,
  
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<pre>sudo apt-get install plink-tutorial</pre>
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<pre>docker run --rm -p 8888:8888 statisticalgenetics/mendelian-randomization</pre>
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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.
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==Pleiotropy and Mediation Analysis==
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Pleiotropy.pdf Pleiotropy Exercise [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Pleiotropy_Outputs.pdf Pleiotropy Output [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy_answers.pdf Pleiotropy Docker Image]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Pleiotropy_Questions.pdf Pleiotropy Questions [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Pleiotropy_Answers.pdf Pleiotropy Answers [PDF]]
  
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To pull and download the docker image from the Docker Hub repository,
  
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==GWAS: Association Analysis Controlling for Population Substructure==
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<pre>docker pull statisticalgenetics/pleiotropy</pre>
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* [http://statgen.us/files/tutorials/gwas-substructure/GWAS_Data_Controlling_for_Substructure.pdf Exercise <nowiki>[PDF]</nowiki>]
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To run the exercise from the downloaded docker image,
  
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====Installing Packages====
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<pre>docker run --rm -p 8888:8888 statisticalgenetics/pleiotropy</pre>
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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 plink-tutorial</pre>
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==PLINK GWAS: Data Quality Control and Association Analysis Controlling for Population Substructure==
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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.
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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://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_Data_QC.pdf PLINK GWAS: Data QC Exercise [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_Data_QC_Outputs.pdf PLINK GWAS: Data QC Output [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_Data_QC_Questions.pdf PLINK GWAS: Data QC Questions [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_Data_QC_Answers.pdf PLINK GWAS: Data QC Answers [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_GWAS_Substructure.pdf PLINK GWAS: Population Substructure Exercise [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_GWAS_Substructure_Outputs.pdf PLINK GWAS: Population Substructure Output [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_GWAS_Substructure_Questions.pdf PLINK GWAS: Population Substructure Questions [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/PLINK_GWAS_Substructure_Answers.pdf PLINK GWAS: Population Substructure Answers [PDF]]
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* [https://hub.docker.com/r/statisticalgenetics/plink-gwas PLINK GWAS Docker Image]
  
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To pull and download the docker image from the Docker Hub repository,
  
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==RV-TDT==
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<pre>docker pull statisticalgenetics/plink-gwas</pre>
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* [http://statgen.us/files/tutorials/rvtdt/rvtdt_exercise.pdf Exercise <nowiki>[PDF]</nowiki>]
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To run the exercise from the downloaded docker image,
  
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====Installing Packages====
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<pre>docker run --rm -p 8888:8888 statisticalgenetics/plink-gwas</pre>
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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 rvtdt-tutorial</pre>
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==Power Analysis==
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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.
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Power_Calculations_Questions.pdf Power Analysis Questions [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Power_Calculations_Answers.pdf Power Analysis Answers [PDF]]
  
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==PSEQ==
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==REGENIE==
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* [http://statgen.us/files/tutorials/pseq/PSEQ_exercise.pdf PSEQ Exercise <nowiki>[PDF]</nowiki>]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regenie.pdf Regenie Exercise [PDF]]
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* [http://statgen.us/files/tutorials/pseq/PSEQ_commands.txt Commands in Excercise]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regenie_Outputs.pdf Regenie Output [PDF]]
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* [https://hub.docker.com/r/statisticalgenetics/regenie Regenie Docker Image]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regenie_Questions.pdf Regenie Questions [PDF]]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regenie_Answers.pdf Regenie Answers [PDF]]
  
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==SEQSpark==
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To pull and download the docker image from the Docker Hub repository,
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* [http://statgen.us/files/tutorials/seqspark/SEQSpark_exercise_Final_v4.pdf SEQSpark Exercise <nowiki>[PDF]</nowiki>]
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* [http://statgen.us/files/images/SEQSpark.ova Virtual Machine Image]
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====Installing Packages====
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<pre>docker pull statisticalgenetics/regenie</pre>
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To install from packages, follow the configuration steps above and run the following command.
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To run the exercise from the downloaded docker image,
  
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<pre>sudo apt-get install seqspark-tutorial</pre>
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<pre>docker run --rm -p 8888:8888 statisticalgenetics/regenie</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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==Variant Association Tools==
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==Regression and Intro to PLINK and R==
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* [http://statgen.us/files/tutorials/vat/VAT_exercise_2018%20with_graphs.pdf VAT 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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====Installing Packages====
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regression.pdf Regression Exercise [PDF]]
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To install from packages, follow the configuration steps above and run the following command.
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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/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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<pre>sudo apt-get install vtools-tutorial</pre>
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To pull and download the docker image from the Docker Hub repository,
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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.
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==Cochran Armitage Trend Test==
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<pre>docker pull statisticalgenetics/regression-plink-r</pre>
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* [http://statgen.us/files/tutorials/Armitage_sample_size_Berlin_1.pdf CATT Exercise <nowiki>[PDF]</nowiki>]
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To run the exercise from the downloaded docker image,
  
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==Population Genetics==
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<pre>docker run --rm -p 8888:8888 statisticalgenetics/regression-plink-r</pre>
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* [http://statgen.us/files/tutorials/population/Popgen_exe_ans.pdf Popgen Exercise <nowiki>[PDF]</nowiki>]
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* [http://statgen.us/files/tutorials/population/popgen_drift.q Commands for popgen_drift]
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* [http://statgen.us/files/tutorials/population/popgen_selection.q Commands for popgen_selection]
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==GATK and IGV==
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==Pencil and Paper Exercise==
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* [http://statgen.us/files/tutorials/Variant_calling_exercices_GATK_IGV.pdf GATK/IGV Exercise <nowiki>[PDF]</nowiki>]
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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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===Software Links===
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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://www.broadinstitute.org/gatk/ GATK]
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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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:::* [http://www.broadinstitute.org/igv/ IGV] ([http://statgen.us/files/software/igv.jar Download JAR file])
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Linkage_Disequilibrium_Answers.pdf Linkage Disequilibrium Answers [PDF]]
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===Result Files===
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:::* [http://statgen.us/files/2016/07/gatk_results.tar.gz GATK/IGV exercise]
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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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