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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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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===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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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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===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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<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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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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sudo add-apt-repository ppa:webupd8team/java
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sudo apt-get update
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</pre>
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==Annotation==
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==FastLMM & GCTA==
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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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* [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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==GenABEL==
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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/genabel/GenABEL_with_PLINK1.9.pdf GenABEL Exercise <nowiki>[PDF]</nowiki>]
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==GWAS: Data Quality Control==
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<pre>docker pull statisticalgenetics/fastlmm-gcta</pre>
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* [http://statgen.us/files/tutorials/gwas-qc/PLINK_data_QC.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/fastlmm-gcta</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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==Mendelian Randomization==
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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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* [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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To pull and download the docker image from the Docker Hub repository,
  
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<pre>docker pull statisticalgenetics/mendelian-randomization</pre>
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To run the exercise from the downloaded docker image,
  
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==GWAS: Association Analysis Controlling for Population Substructure==
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<pre>docker run --rm -p 8888:8888 statisticalgenetics/mendelian-randomization</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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====Installing Packages====
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==Pleiotropy and Mediation Analysis==
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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/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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<pre>sudo apt-get install plink-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/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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<pre>docker pull statisticalgenetics/pleiotropy</pre>
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To run the exercise from the downloaded docker image,
  
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<pre>docker run --rm -p 8888:8888 statisticalgenetics/pleiotropy</pre>
  
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==RV-TDT==
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==PLINK GWAS: Data Quality Control and Association Analysis Controlling for Population Substructure==
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* [http://statgen.us/files/tutorials/rvtdt/rvtdt_exercise.pdf 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/PLINK_Data_QC.pdf PLINK GWAS: Data QC 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/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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<pre>sudo apt-get install rvtdt-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/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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==PSEQ==
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<pre>docker pull statisticalgenetics/plink-gwas</pre>
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* [http://statgen.us/files/tutorials/pseq/PSEQ_exercise.pdf PSEQ Exercise <nowiki>[PDF]</nowiki>]
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To run the exercise from the downloaded docker image,
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* [http://statgen.us/files/tutorials/pseq/PSEQ_commands.txt Commands]
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==SEQSpark==
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<pre>docker run --rm -p 8888:8888 statisticalgenetics/plink-gwas</pre>
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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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==Power Analysis==
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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/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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<pre>sudo apt-get install seqspark-tutorial</pre>
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==REGENIE==
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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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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regenie.pdf Regenie Exercise [PDF]]
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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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* [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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==Variant Association Tools==
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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/vat/VAT_exercise_2018%20with_graphs.pdf VAT Exercise <nowiki>[PDF]</nowiki>]
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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 vtools-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/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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==Regression and Intro to PLINK and R==
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* [http://statgen.us/files/tutorials/Armitage_sample_size_Berlin_1.pdf CATT 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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==Population Genetics==
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regression.pdf Regression Exercise [PDF]]
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* [http://statgen.us/files/tutorials/population/Popgen_exe_ans.pdf Popgen Exercise <nowiki>[PDF]</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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* [http://statgen.us/files/tutorials/population/popgen_drift.q Commands for popgen_drift]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regression_Questions.pdf Regression Questions [PDF]]
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* [http://statgen.us/files/tutorials/population/popgen_selection.q Commands for popgen_selection]
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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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==GATK and IGV==
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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/Variant_calling_exercices_GATK_IGV.pdf GATK/IGV Exercise <nowiki>[PDF]</nowiki>]
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====Software Links====
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<pre>docker pull statisticalgenetics/regression-plink-r</pre>
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:* [https://www.broadinstitute.org/gatk/ GATK]
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To run the exercise from the downloaded docker image,
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:* [http://www.broadinstitute.org/igv/ IGV] ([http://statgen.us/files/software/igv.jar Download JAR file])
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====Result Files====
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<pre>docker run --rm -p 8888:8888 statisticalgenetics/regression-plink-r</pre>
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:* [http://statgen.us/files/2016/07/gatk_results.tar.gz GATK/IGV exercise]
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==Regression==
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==Pencil and Paper Exercise==
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* [http://statgen.us/files/tutorials/regression_exercise.pdf Regression 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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* [[Regression_Exercise|Commands in Exercise]]
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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]]

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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