Statistical Genetics Courses - New pages [en]

Previous Courses

2026-08-17T19:19:50Z

Serveradmin: /* Course Exercise Commands */

==[[CourseExerciseScripts|Course Exercise Commands]]==
Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses

For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions

==2025 Courses==
* [[Advgenemap2025|Advanced Gene Mapping]]
* [[ComplexNGS2025|Genetic Association Course]]
* [https://github.com/statgenetics/statgen-courses/blob/master/release/AGMC_course_slides_2025.pdf Lecture Slides]
* [https://github.com/statgenetics/statgen-courses/blob/master/release/AGMC_2025_exercise_booklet.pdf Exercises]

==2024 Courses==
* [[Advgenemap2024|Advanced Gene Mapping]]
* [[Genassoc2024|Genetic Association Course]]
* [https://statgen.us/files/2024/04/AGMC_lecture_booklet.pdf Lecture Slides]
* [https:///statgen.us/files/2024/04/AGMC_2024_excerise_booklet.pdf Exercises]

==2023 Courses==
* [[Advgenemap2023|Advanced Gene Mapping]]
* [[ComplexNGS2023|Complex Trait Analysis of Next Generation Sequence Data]]
* [https://statgen.us/files/2023/05/Lecture_booklet.pdf Lecture Slides]
* [https://statgen.us/files/2023/05/Exercise_booklet_AGMC_May_23.pdf Exercises]

==2022 Courses==
* [[Advgenemap2022|Advanced Gene Mapping]] (Oneline due to COVID)
* [[AdvgenemapNov2022|Advanced Gene Mapping]] (Nov. 2022)
* [https://statgen.us/files/2022/11/Lectures_AGMC_November_2022.pdf Lecture Slides]
* [https://statgen.us/files/2022/11/Exercise_booklet_AGMC_11_11_22.pdf Exercises]
* [[Genassoc2022|Genetic Association]]
* [https://statgen.us/files/2022/09/Exercise_booklet_9_26_22.pdf Exercises]

==2021 Courses==
* [[Advgenemap2021|Advanced Gene Mapping]] (Online due to COVID)
* [[Genassoc2021|Genetic Association]] (Cancelled due to COVID19 restrictions)
* [[ComplexNGS2021|Complex Trait Analysis of Next Generation Sequence Data]]

==2020 Courses==
* [[Advgenemap2020|Advanced Gene Mapping]]
* [[Genassoc2020|Genetic Association]] (Cancelled due to COVID)
* [[ComplexNGS2020|Complex Trait Analysis of Next Generation Sequence Data]] (Cancelled due to COVID)

==2019 Courses==
* [[ComplexNGS2019|Complex Trait Analysis of Next Generation Sequence Data]]
* [[Genassoc2019|Genetic Association]]
* [[Advgenemap2019|Advanced Gene Mapping]]

==2018 Courses==
* [[Genassoc2018|Genetic Association]]
* [[ComplexNGS2018|NGS Analysis of Complex Traits]]
* [[Advgenemap2018|Advanced Gene Mapping]]

==2017 Courses==
* [[NGSMendelian2017|NGS Analysis of Mendelian Traits]]
* [[Genassoc2017|Genetic Association]]
* [[ComplexNGS2017|NGS Analysis of Complex Traits]]
* [[Advgenemap2017|Advanced Gene Mapping]]

==2016 Courses==
* [[NGSMendelian2016|NGS Analysis of Mendelian Traits - MDC Berlin]]
* [[Genassoc2016|Genetic Association -MDC Berlin]]
* [[ComplexNGS2016|NGS Analysis of Complex Traits- MDC Berlin]]
* [[Advgenemap2016|Advanced Gene Mapping - Rockefeller NYC]]

==2015 Courses==
* [[2015SeptMDC|NGS Analysis of Mendelian Traits - MDC Berlin]]
* [https://statgen.uni-koeln.de/courses/locations/germany/genetic-association-course-in-2015.php/Genetic Genetic Association- MDC Berlin]]
* [[2015MarchMDC|NGS Analysis of Complex Traits -MDC Berlin]]
* [[2015AdvancedGeneMapping|Advanced Gene Mapping - Rockefeller NYC]]

==2014 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/genetic-association-course-in-2014.php/ Genetic Association Course - MDC Berlin March 2014]
* [https://statgen.uni-koeln.de/courses/locations/germany/next-generation-sequence-data-analysis-course-in-2014.php/ Next Generation Sequence Data Analysis Course - MDC Berlin June 2014]

==2013 Course==
[https://statgen.uni-koeln.de/courses/locations/germany/genetic-association-course-in-2013.php/ Genetic Association Course - Berlin: June 2013]

==2012 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/genetic-association-course-in-2012.php/ Genetic Association Course - MDC Berlin July 2012]
* [https://statgen.uni-koeln.de/courses/locations/germany/gene-mapping-course-in-2012.php/ Gene Mapping Course - MDC Berlin November 2012]

==2011 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/genetic-association-course-in-2011.php/ Genetic Association Course - MDC Berlin July 2011]
* [https://statgen.uni-koeln.de/courses/locations/germany/gene-mapping-course-in-2011.php/ Gene Mapping Course -MDC Berlin November 2011]

==2010 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/genetic-association-course-in-2010.php/ Genetic Association Course - MDC Berlin May 2010]
* [https://statgen.uni-koeln.de/courses/locations/germany/gene-mapping-course-in-2010.php/ Gene Mapping Course - MDC Berlin October 2010]

==2009 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/gene-mapping-course-in-2009.php Gene Mapping Course - MDC Berlin: November 2009]

==2008 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/gene-mapping-course-in-2008.php/ Basic Gene Mapping Course - MDC Berlin: July 2008]

==2007 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/gene-mapping-course-in-2007.php/ Basic Gene Mapping Course - MDC Berlin: July 2007]

==2006 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/gene-mapping-course-in-2006.php/ Basic Gene Mapping Course - MDC Berlin: July 2006]

==2005 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/gene-mapping-course-in-2005.php/ Basic Gene Mapping Course - MDC Berlin July 2005]

==2004 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/gene-mapping-course-in-2004.php/ Basic Gene Mapping Course - MDC July 2004]

==2003 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/gene-mapping-course-in-2003.php Basic Gene Mapping Course - MDC Berlin: July 2003]

Previous Tutorials Software

2026-08-17T17:08:18Z

Serveradmin: /* Tutorials for Previous Courses */

==Tutorials for Previous Courses==
* [[Previous_Tutorials_Software#Annotation|ANNOVAR Annotation]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/annovar.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/annovar/tags docker image]
* [[Previous_Tutorials_Software#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[Previous_Tutorials_Software#FastLMM | Family-based Association using FaST-LMM, PLINK and R]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/fastlmm-gcta.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta/tags docker image]
* [[Previous_Tutorials_Software#IGV|IGV]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/igv.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/igv/tags docker image]
* [[Previous_Tutorials_Software#Gemini|Gemini]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/gemini.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/gemini/tags docker image]
* [[Previous_Tutorials_Software#GCTA|GCTA]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/fastlmm-gcta.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta/tags docker image]
* [[Previous_Tutorials_Software#GWAS:_Data_Quality_Control|GWAS: QC]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/plink.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/plink/tags docker image]
* [[Previous_Tutorials_Software#GWAS:_Association_Analysis_Controlling_for_Population_Substructure|GWAS: Controlling for Population Substructure]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/plink.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/plink/tags docker image]
* [[Previous_Tutorials_Software#Epistasis_.28PLINK_and_CASSI.29 | Interaction analysis using PLINK and CASSI]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/epistasis.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/epistasis/tags docker image]
* [[Previous_Tutorials_Software#Linkage.2FFastLinkage|LINKAGE]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/mlink.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/mlink/tags docker image]
* [[Previous_Tutorials_Software#Population_Genetics|Population Genetics]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/popgen.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/popgen/tags docker image]
* [[Previous_Tutorials_Software#Pleiotropy|Pleiotropy]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/pleiotropy.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/pleiotropy/tags docker image]
* [[Previous_Tutorials_Software#Polygenic_risk_prediction_.28NPS_method.29|Polygenic risk prediction using non-parametric shrinkage]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/nps.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/nps/tags docker image]
* [[Previous_Tutorials_Software#PSEQ|PLINK/SEQ (PSEQ)]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/pseq.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/pseq/tags docker image]
* [[Previous_Tutorials_Software#R_and_PLINK|R and PLINK exercise]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/plink-r-nothnagel.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/plink-r-nothnagel/tags docker image]
* [[Previous_Tutorials_Software#Regression|Regression]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/regression.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/regression/tags docker image]
* [[Previous_Tutorials_Software#RV-TDT|RV-TDT]]
* [[Previous_Tutorials_Software#SEQLinkage|SEQLinkage]]
* [[Previous_Tutorials_Software#SEQSpark|SEQSpark]]
* [[Previous_Tutorials_Software#SLINK|SLINK]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/slink.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/slink/tags docker image]
* [[Previous_Tutorials_Software#Variant_Association_Tools|Variant Association Tools]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/vat.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/vat/tags docker image]



==Running Tutorials on Your Computer==
Starting Fall 2019 we adopt [https://www.docker.com/ docker] to run our course material . We have created various [https://hub.docker.com/u/statisticalgenetics docker repositories] with source material freely available from [https://github.com/statgenetics/statgen-courses github] for users to readily setup and reproduce our tutorials on their own computers. These docker images can also be used as production tool to run relevant software on your computer (Mac, Linux or Windows) or even a high performance computing cluster (if properly configured) for your own data analysis.

===General instructions===
* [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#alternative-to-cloud-server-use-your-own-computer Instructions to setup course tutorial environment on your computer]
* [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#option-1-launch-exercise-in-jupyterlab Instructions to run course tutorial through JupyterLab]
* [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#option-2-launch-from-command-shell Instructions to run course tutorial through command line terminal]

===Preparing Your Computer===
{| class="wikitable"
|-
||{{#ev:youtube|3K-sGzxsyK0|240|center|Linux}}
||{{#ev:youtube|DRCDNBlxZ-w|240|center|Mac}}
||{{#ev:youtube|sxv45NCSFMk|240|center|Windows}}
|}

===Running Exercises===
{{#ev:youtube|OgHvRVtIIog|320}}

===Tutorial specific instructions===
We use a script [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup "statgen-setup"] to start the docker based environments for these tutorials. Please refer to the previous section for instructions on the installation of this script.

Material and instructions for specific exercise are listed in each section below (''only those using statgen-setup command are relevant to our docker based tutorials''). They provide links to materials and a minimal set of commands to use for launching and running an exercise. Command "statgen-setup login" will allow you to start and login to a Linux command line environment (regardless of your current computational environment) to perform all analysis in command shells. This works for all the tutorials on this page. Additionally, some tutorials support command "statgen-setup launch" which will start a JupyterLab server to perform the analysis.

==Alohomora==
* [http://statgen.us/files/tutorials/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]

==Annovar complex traits==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.pdf Functional Annotation Exercise <nowiki>[PDF]</nowiki>]
* [[Commands in Annotation Exercise|Exercise Commands]]

To run the exercise from docker image provided,

<pre>statgen-setup login --tutorial annovar
</pre>

==Annovar Mendelian traits==
* [http://statgen.us/files/tutorials/FunctionalAnnotation_Annovar_final.pdf Exercise <nowiki>[PDF]</nowiki>]
* [https://statgen.us/files/2017/09/commands/annovar-functional_annotation.txt Commands Part I - Functional Annotation]
* [https://statgen.us/files/2017/09/commands/annovar-variant_filtering.txt Commands Part II - Variant Filtering]

==Cochran Armitage Trend Test==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Armitage_sample_size.pdf CATT Exercise <nowiki>[PDF]</nowiki>]

==Epistasis (PLINK and CASSI)==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Epistasis_PLINK_CASSI.pdf Epistasis exercise <nowiki>[PDF]</nowiki>]

To run the exercise from docker image provided,

<pre>statgen-setup login --tutorial epistasis
</pre>

==FastLMM==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FASTLMM.pdf FastLMM exercise <nowiki>[PDF]</nowiki>]

To run the exercise from docker image provided,

<pre>statgen-setup login --tutorial fastlmm-gcta
</pre>

==Fine-mapping (SuSiE method)==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/finemapping.docx susieR Exercise <nowiki>[DOCX]</nowiki>]
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/finemapping_answers.docx susieR Exercise Answers <nowiki>[DOCX]</nowiki>]
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/finemapping.ipynb susieR Exercise <nowiki>[Ipython notebook]</nowiki>]
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/finemapping_answers.ipynb susieR Exercise Answers <nowiki>[Ipython notebook]</nowiki>]

To run the exercise from docker image provided,

<pre>statgen-setup launch --tutorial finemap
</pre>

==GCTA==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/GCTA.pdf GCTA exercise <nowiki>[PDF]</nowiki>]

To run the exercise from docker image provided,

<pre>statgen-setup login --tutorial fastlmm-gcta
</pre>

==Gemini==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Gemini.docx Gemini exercise <nowiki>[DOCX]</nowiki>]

To run the exercise from docker image provided,

<pre>statgen-setup login --tutorial gemini
</pre>

==Genehunter==
* [http://statgen.us/files/tutorials/genehunter/Mult_Genehunter.pdf <nowiki>[PDF]</nowiki>]
* [[Genehunter Exercise|Exercise Commands]]

To install from packages, follow the configuration steps above and run the following command.

<pre>sudo apt-get install genehunter-tutorial</pre>
The exercise's files will then be installed in the folder ''/home/shared/genehunter''. You can run from there or copy the files into your user's home directory and proceed with the exercise.

==GWAS: Data Quality Control==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_data_QC.pdf Exercise <nowiki>[PDF]</nowiki>]
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PLINK_Data_QC.ipynb Exercise <nowiki>[IPython Notebook]</nowiki>]
* [[GWAS Data QC Exercise|Exercise Commands]]

To run the exercise via JupyterLab from docker image provided,

<pre>statgen-setup launch --tutorial plink
</pre>

Alternatively, you can opt to run the exercise via command terminal from docker image provided,

<pre>statgen-setup login --tutorial plink
</pre>

==GWAS: Association Analysis Controlling for Population Substructure==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_Substructure.pdf Exercise <nowiki>[PDF]</nowiki>]
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PLINK_Substructure.ipynb Exercise <nowiki>[IPython Notebook]</nowiki>]
* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]

To run the exercise via JupyterLab from docker image provided,

<pre>statgen-setup launch --tutorial plink
</pre>

Alternatively, you can opt to run the exercise via command terminal from docker image provided,

<pre>statgen-setup login --tutorial plink
</pre>

==Homozygosity Mapper==
* [http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_1.pdf Exercise Part I]
* [http://statgen.us/files/tutorials/Homozygosity_mapping_exercise_part_2.pdf Exercise Part II]
* [http://www.homozygositymapper.org Data Sets]

==IGV==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/IGV.docx IGV exercise <nowiki>[DOCX]</nowiki>]
* [http://statgen.us/files/igv_exercise.zip Exercise files (VCF and BAM)]

==Linkage/FastLinkage==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/MLINK.pdf LINKAGE Exercise <nowiki>[DOCX]</nowiki>]

To run the exercise from docker image provided,

<pre>statgen-setup login --tutorial mlink
</pre>

==LD clumping==
* [https://github.com/cumc/bioworkflows/blob/master/GWAS/LD_Clumping.ipynb LD Clumping Exercise <nowiki>[IPython Notebook]</nowiki>]

To run the exercise from docker image provided,

<pre>statgen-setup launch --tutorial clumping
</pre>

==MR-JTI for TWAS==
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/MR_JTI.ipynb MR-JTI Exercise <nowiki>[IPython Notebook]</nowiki>]

To run the exercise from docker image provided,

<pre>statgen-setup launch --tutorial twas
</pre>

==Pleiotropy==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy.pdf Pleiotropy Exercise <nowiki>[PDF]</nowiki>]
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy_answers.pdf Pleiotropy Answers to Questions <nowiki>[PDF]</nowiki>]

To run the exercise from docker image provided,

<pre>statgen-setup login --tutorial pleiotropy
</pre>

==Polygenic risk prediction (NPS method)==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/NPS.pdf PRS NPS Exercise <nowiki>[DOCX]</nowiki>]

To run the exercise from docker image provided,

<pre>statgen-setup login --tutorial nps
</pre>

==Polygenic risk prediction (LDpred2 method)==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/ldpred2_example.pdf PRS LDpred2 Exercise <nowiki>[PDF]</nowiki>]
* [https://github.com/cumc/bioworkflows/blob/master/ldpred/ldpred2_example.ipynb PRS LDpred2 Exercise <nowiki>[Ipython Notebook]</nowiki>]

To run the exercise from docker image provided,

<pre>statgen-setup launch --tutorial ldpred2
</pre>

Then follow prompts on the terminal output to open up the JupyterLab server in your web browser. If it is the first time you start this server, please open a command terminal inside JupyterLab, and type

<pre>get-data</pre>

to load the data-set to the JupyterLab workspace.


==Population Genetics==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PopGen.docx Popgen Exercise <nowiki>[DOCX]</nowiki>]

To run the exercise from docker image provided,

<pre>statgen-setup login --tutorial popgen
</pre>

==PSEQ==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PSEQ.pdf PSEQ Exercise <nowiki>[PDF]</nowiki>]
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PSEQ.ipynb PSEQ Exercise <nowiki>[Ipython Notebook]</nowiki>]

To run the exercise from docker image provided,

<pre>statgen-setup launch --tutorial pseq
</pre>

Notice that since PSEQ exercise does not involve generating and visualizing plots, it is also fine to use a command terminal, instead of the JupyterLab server, to run this exercise and reproduce exactly what was described in the tutorial. To do so,

<pre>statgen-setup login --tutorial pseq
</pre>

==R and PLINK==
To run the exercise from docker image provided,

<pre>statgen-setup launch --tutorial plink-r-nothnagel
</pre>

==REGENIE==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/regenie_example.pdf REGENIE Exercise <nowiki>[PDF]</nowiki>]
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/regenie_example.ipynb REGENIE Exercise <nowiki>[Ipython Notebook]</nowiki>]

To run the exercise from docker image provided,

<pre>statgen-setup launch --tutorial regenie
</pre>

Then follow prompts on the terminal output to open up the JupyterLab server in your web browser. If it is the first time you start this server, please open a command terminal inside JupyterLab, and type

<pre>get-data</pre>

to load the data-set to the JupyterLab workspace.

==Regression==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/regression.docx Regression Exercise <nowiki>[DOCX]</nowiki>]
* [[Regression_Exercise|Exercise Commands]]

To run the exercise from docker image provided,

<pre>statgen-setup login --tutorial regression
</pre>

==RV-TDT==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/RV-TDT.doc Exercise <nowiki>[DOC]</nowiki>]
* [[RV-TDT|Exercise Commands]]

====Installing Packages====
To install from packages, follow the configuration steps above and run the following command.

<pre>sudo apt-get install rvtdt-tutorial</pre>
The exercise's files will then be installed in the folder ''/home/shared/rvtdt''. You can run from there or copy the files into your user's home directory and proceed with the exercise.

==SEQLinkage==
* [http://statgen.us/files/tutorials/SEQLinkage/SEQLinkage_revised_with_pg_numb.pdf SEQLinkage Exercise <nowiki>[PDF]</nowiki>]
* [[SEQLinkage_Commands_in_Exercise|Exercise Commands]]

To install from packages, follow the configuration steps above and run the following command.

<pre>sudo apt-get install seqlinkage-tutorial</pre>
The exercise's files will then be installed in the folder ''/home/shared/seqlinkage''. You can run from there or copy the files into your user's home directory and proceed with the exercise.

==SEQSpark==
* [http://statgen.us/files/tutorials/seqspark/SEQSpark_exercise_Final_v4.pdf SEQSpark Exercise <nowiki>[PDF]</nowiki>]
* [[SEQSpark|Exercise Commands]]
* [http://statgen.us/files/images/SEQSpark.ova Virtual Machine Image]

====Installing Packages====
To install from packages, follow the configuration steps above and run the following command.

<pre>sudo apt-get install seqspark-tutorial</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==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Slink.doc SLINK Exercise <nowiki>[DOCX]</nowiki>]

To run the exercise from docker image provided,

<pre>statgen-setup login --tutorial slink</pre>

==SUPERLINK==
* [http://statgen.us/files/tutorials/Superlink_Exercise_v2.pdf SUPERLINK Exercise <nowiki>[PDF]</nowiki>]
* [https://statgen.research.bcm.edu/files/2016/10/data/superlink.zip Superlink]

==Variant Association Tools==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/VAT.docx VAT Exercise <nowiki>[DOCX]</nowiki>]
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/VAT.ipynb VAT Exercise <nowiki>[Ipython notebook]</nowiki>]

To run the exercise from docker image provided,

<pre>statgen-setup launch --tutorial vat
</pre>

Then follow the prompts on the terminal output to open up the JupyterLab server in your web browser. You should find the exercise notebook in the side panel, and you can click to open it.