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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]]
 +
* [[Tutorials#Pleiotropy|Pleiotropy]]
 +
* [[Tutorials#PLINK_GWAS:_Data_Quality_Control_and Association_Analysis_Controlling_for_Population_Substructure|PLINK GWAS: QC and Controlling for Population Substructure]]
 +
* [[Tutorials#Power_Analysis|Power Analysis]]
 +
* [[Tutorials#REGENIE|REGENIE]]
 +
* [[Tutorials#Regression_and_Intro_to_PLINK_and_R|Regression and Intro to PLINK and R]]
 +
* [[Tutorials#Pencil_and_Paper_Exercise|Pencil and Paper Exercise]]
 +
 
==Running Tutorials on Your Computer==
 
==Running Tutorials on Your Computer==
−
We have created a debian repository to make it easier to use our tutorials. This repository allows you to install all required software and example data included in tutorials on your computer. Using this repository will require that you have administrator access to a computer with Linux System. If you don't have this level of access or your computer running non-Linux systems (Windows or OS), you have two options. First, you could install the repository on a remote cloud serve, such as [https://www.vultr.com/ VULTR]. Second, you can install a Virtual Machine program (such as [https://www.virtualbox.org/ VirtualBox]) on your computer, and then load our pre-configured virtual machine image (VM Image) into the Virtual Machine. You can refer to these online videos [[VirtualBox Installation|here]] to install VirtualBox on your computer.
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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. 
−
 
+
−
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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To install the repository on the cloud server, virtual machine, or your own computer, you need to follow these configuration steps. Please run as the root user or using the sudo command.
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<pre>echo "deb [trusted=yes] https://statgen.research.bcm.edu/deb ./" | sudo tee -a /etc/apt/sources.list.d/statgen.list
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sudo add-apt-repository -y ppa:webupd8team/java
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sudo apt-get update
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</pre>
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We have made a video tutorial to show you how to install the repository step by step which is available [https://www.youtube.com/watch?v=5jRJHXxkC9g&t=19s here]. If you want to install specific exercise at your demands, please refer to commands listed in each section below.
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−
 
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==Alohorma==
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* [http://statgen.us/files/tutorials/seqspark/Alohomora_Exercise_revised.pdf Exercise <nowiki>[PDF]</nowiki>]
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* [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Data Set]
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−
* [http://gmc.mdc-berlin.de/alohomora/ Software Link]
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−
 
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==Annotation==
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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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* [[Commands in Annotation Exercise|Exercise Commands]]
+
−
 
+
−
To install from packages, follow the configuration steps above and run the following command.
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−
 
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<pre>sudo apt-get install annotation-tutorial</pre>
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−
The exercise's files will then be installed in the folder ''/home/shared/functional_annotation''. You can run from there or copy the files into your user's home directory and proceed with the exercise.
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−
 
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==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]
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* [https://statgen.research.bcm.edu/files/2017/09/commands/annovar-variant_filtering.txt Commands Part II - Variant Filtering]
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−
 
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==Cochran Armitage Trend Test==
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* [http://statgen.us/files/tutorials/Armitage_sample_size_Berlin_1.pdf CATT Exercise <nowiki>[PDF]</nowiki>]
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−
 
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==GATK and IGV==
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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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−
 
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====Software Links====
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:* [https://www.broadinstitute.org/gatk/ GATK]
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:* [http://www.broadinstitute.org/igv/ IGV] ([http://statgen.us/files/software/igv.jar Download JAR file])
+
−
 
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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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−
 
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==Gemini==
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* [https://drive.google.com/file/d/0B2pJ9cgevF3sTS1DeGxYalFTN00/view Bam files for exercise]
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−
 
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==GenABEL==
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* [http://statgen.us/files/tutorials/genabel/GenABEL_with_PLINK1.9.pdf GenABEL Exercise <nowiki>[PDF]</nowiki>]
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* [[GeneABEL Exercise|Exercise Commands]]
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−
 
+
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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 genabel-tutorial</pre>
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===General instructions===
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The exercise's files will then be installed in the folder ''/home/shared/genabel''. You can run from there or copy the files into your user's home directory and proceed with the exercise.
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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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==Genehunter==
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===Tutorial specific instructions===
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* [http://statgen.us/files/tutorials/genehunter/Mult_Genehunter.pdf <nowiki>[PDF]</nowiki>]
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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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* [[Genehunter Exercise|Exercise Commands]]
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==GWAS: Data Quality Control==
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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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* [http://statgen.us/files/tutorials/gwas-qc/PLINK_data_QC.pdf Exercise <nowiki>[PDF]</nowiki>]
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* [[GWAS Data QC Exercise|Exercise Commands]]
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−
====Installing Packages====
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==FastLMM & GCTA==
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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/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]]
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* [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta FastLMM & GCTA Docker Image]
  
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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_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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==GWAS: Association Analysis Controlling for Population Substructure==
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<pre>docker pull statisticalgenetics/fastlmm-gcta</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,
−
* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]
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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==
−
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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* [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]]
  
−
==Homozygosity Mapper==
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To pull and download the docker image from the Docker Hub repository,
−
*[http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_1.pdf Exercise Part I]
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*[http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_2.pdf Exercise Part II]
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−
*[http://www.homozygositymapper.org Data Sets]
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==IGV==
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<pre>docker pull statisticalgenetics/mendelian-randomization</pre>
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*[https://statgen.research.bcm.edu/files/software/igv/igv-2.3.97.jar igv.jar Software Link]
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To run the exercise from the downloaded docker image,
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*[https://statgen.research.bcm.edu/files/2017/09/data/igv_exercise.zip BAM and VCF Files]
+
  
−
==Linkage/FastLinkage==
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<pre>docker run --rm -p 8888:8888 statisticalgenetics/mendelian-randomization</pre>
−
* [http://statgen.us/files/tutorials/SEQLinkage/linkage_intro_ex_berlin_2018_with_pg_num.pdf Linkage Introduction <nowiki>[PDF]</nowiki>]
+
  
−
<!--
+
==Pleiotropy and Mediation Analysis==
−
==Population Genetics==
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Pleiotropy.pdf Pleiotropy Exercise [PDF]]
−
* [http://statgen.us/files/tutorials/population/berlinseq.2.2.PopGen_exercise.pdf Population Exercise <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Pleiotropy_Outputs.pdf Pleiotropy Output [PDF]]
−
* [http://statgen.us/files/tutorials/population/berlinseq.2.2.PopGen_answers.pdf Exercise Answers <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy_answers.pdf Pleiotropy Docker Image]
−
* [http://statgen.us/files/tutorials/population/popgen_drift.q Commands for popgen_drift]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Pleiotropy_Questions.pdf Pleiotropy Questions [PDF]]
−
* [http://statgen.us/files/tutorials/population/popgen_selection.q Commands for popgen_selection]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Pleiotropy_Answers.pdf Pleiotropy Answers [PDF]]
−
-->
+
−
==Population Genetics==
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−
* [http://statgen.us/files/tutorials/population/Popgen_exe_ans.pdf Popgen Exercise <nowiki>[PDF]</nowiki>]
+
−
* [http://statgen.us/files/tutorials/population/popgen_drift.q R Script for popgen_drift]
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−
* [http://statgen.us/files/tutorials/population/popgen_selection.q R Script for popgen_selection]
+
  
−
==PSEQ==
+
To pull and download the docker image from the Docker Hub repository,
−
* [http://statgen.us/files/tutorials/pseq/PSEQ_exercise.pdf PSEQ Exercise <nowiki>[PDF]</nowiki>]
+
−
* [[PSEQ Commands in Exercise|Exercise Commands]]
+
  
−
To install from packages, follow the configuration steps above and run the following command.
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<pre>docker pull statisticalgenetics/pleiotropy</pre>
 +
To run the exercise from the downloaded docker image,
  
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<pre>sudo apt-get install plinkseq-tutorial</pre>
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<pre>docker run --rm -p 8888:8888 statisticalgenetics/pleiotropy</pre>
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The exercise's files will then be installed in the folder ''/home/shared/pseq''. You can run from there or copy the files into your user's home directory and proceed with the exercise.
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−
==Regression==
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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/regression_exercise.pdf Regression 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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* [[Regression_Exercise|Exercise Commands]]
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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.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]
  
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<pre>sudo apt-get install regression-tutorial</pre>
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To pull and download the docker image from the Docker Hub repository,
−
The exercise's files will then be installed in the folder ''/home/shared/regression''. You can run from there or copy the files into your user's home directory and proceed with the exercise.
+
  
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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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* [[RV-TDT|Exercise Commands]]
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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]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Power_Calculations_Answers.pdf Power Analysis Answers [PDF]]
  
−
==SEQLinkage==
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==REGENIE==
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* [http://statgen.us/files/tutorials/SEQLinkage/SEQLinkage_revised_with_pg_numb.pdf SEQLinkage Exercise <nowiki>[PDF]</nowiki>]
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regenie.pdf Regenie Exercise [PDF]]
−
* [[SEQLinkage_Commands_in_Exercise|Exercise Commands]]
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* [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]]
  
−
==SEQSpark==
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To pull and download the docker image from the Docker Hub repository,
−
* [http://statgen.us/files/tutorials/seqspark/SEQSpark_exercise_Final_v4.pdf SEQSpark Exercise <nowiki>[PDF]</nowiki>]
+
−
* [[SEQSpark|Exercise Commands]]
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* [http://statgen.us/files/images/SEQSpark.ova Virtual Machine Image]
+
  
−
====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.
+
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>
−
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
+
−
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==
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==Regression and Intro to PLINK and R==
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* [http://statgen.us/files/tutorials/seqspark/slink_ex_short.pdf SLINK Exercise <nowiki>[PDF]</nowiki>]
+
These exercises run using a shared docker image, however the exercises are split into two separate notebooks.
  
−
==SUPERLINK==
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* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regression.pdf Regression Exercise [PDF]]
−
* [http://statgen.us/files/tutorials/Superlink_Exercise_v2.pdf SUPERLINK Exercise <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regression_Outputs.pdf Regression Output [PDF]]
−
* [https://statgen.research.bcm.edu/files/2016/10/data/superlink.zip Superlink]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regression_Questions.pdf Regression Questions [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Regression_Answers.pdf Regression Answers [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Intro_Plink_R.pdf Intro to PLINK & R Exercise [PDF]]
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handouts_2026/Intro_Plink_R_Outputs.pdf Intro to PLINK & R Output [PDF]]
 +
* [https://hub.docker.com/r/statisticalgenetics/regression-plink-r Regression and Intro to PLINK & R Docker Image]
  
−
==Variant Association Tools==
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To pull and download the docker image from the Docker Hub repository,
−
* [http://statgen.us/files/tutorials/VAT_exercise_2018_nographs.pdf VAT Exercise <nowiki>[PDF]</nowiki>]
+
−
* [[VAT Commands in Exercise|Exercise Commands]]
+
  
−
====Installing Packages====
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<pre>docker pull statisticalgenetics/regression-plink-r</pre>
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To install from packages, follow the configuration steps above and run the following command.
+
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/regression-plink-r</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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==VAT Mendelian==
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==Pencil and Paper Exercise==
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* [http://statgen.us/files/tutorials/VAT_Mendelian.pdf 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]]
−
* [[VAT mendelian commands|Exercise Commands]]
+
* [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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