* [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]
===Tutorial specific instructions===
Material and instructions for specific exercise are listed in each section below (''only those using statgen-setup command are relevant to our docker based tutorials''). They provide links to materials and a minimal set of commands to use for launching and running an exercise.
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.
==Alohomora==
==Annotation==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.docx pdf Functional Annotation Exercise <nowiki>[DOCX]</nowiki>]
* [[Commands in Annotation Exercise|Exercise Commands]]
</pre>
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
==Annovar MEndelian==
* [http://statgen.us/files/tutorials/FunctionalAnnotation_Annovar_final.pdf Exercise <nowiki>[PDF]</nowiki>]
* [https://statgen.research.bcm.eduus/files/2017/09/commands/annovar-functional_annotation.txt Commands Part I - Functional Annotation]* [https://statgen.research.bcm.eduus/files/2017/09/commands/annovar-variant_filtering.txt Commands Part II - Variant Filtering]
==Cochran Armitage Trend Test==
<pre>statgen-setup login --tutorial epistasis
</pre>
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
</pre>
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
==GCTA==
</pre>
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
==Gemini==
<pre>statgen-setup login --tutorial gemini
</pre>
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
<pre>statgen-setup login --tutorial plink
</pre>
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
<pre>statgen-setup login --tutorial plink
</pre>
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
* [http://statgen.us/files/igv_exercise.zip Exercise files (VCF and BAM)]
To run the exercise from docker image provided,
<pre>statgen-setup login --tutorial igv
</pre>
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
==Linkage/FastLinkage==
</pre>
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
==Pleiotropy==
</pre>
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
==Polygenic risk prediction (NPS method)==
</pre>
The "statgen-setup" script is available ==Polygenic risk prediction (LDpred2 method)==* [https://github.com/statgenetics/statgen-courses/blob/master/srchandout/statgen-setup hereldpred2_example.pdf PRS LDpred2 Exercise <nowiki>[PDF] and can be installed following </nowiki>]* [https://github.com/statgeneticscumc/statgen-coursesbioworkflows/blob/master/READMEldpred/ldpred2_example.md#prepareipynb PRS LDpred2 Exercise <nowiki>[Ipython Notebook]</nowiki>] To run the exercise from docker image provided, <pre>statgen-yoursetup launch -computer-tutorial ldpred2</pre> Then follow prompts on the terminal output toopen 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-manage-data</pre> to load thedata-tutorials these instructions]set to the JupyterLab workspace.
<!--
</pre>
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
==PSEQ==
</pre>
The "statgen-setup" script is available ==REGENIE==* [https://github.com/statgenetics/statgen-courses/blob/master/srchandout/statgen-setup hereregenie_example.pdf REGENIE Exercise <nowiki>[PDF] and can be installed following </nowiki>]* [https://github.com/statgenetics/statgen-courses/blob/master/READMEnotebooks/regenie_example.md#prepareipynb REGENIE Exercise <nowiki>[Ipython Notebook]</nowiki>] To run the exercise from docker image provided, <pre>statgen-yoursetup launch -computer-tutorial regenie</pre> Then follow prompts on the terminal output toopen 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-manage-data</pre> to load thedata-tutorials these instructions]set to the JupyterLab workspace.
==Regression==
</pre>
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
==RV-TDT==
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
==Variant Association Tools==
* [https://statgenetics.github.iocom/statgenetics/statgen-courses/notebooksblob/master/VAT.html docx VAT Exercise <nowiki>[HTMLDOCX]</nowiki>]* [[https://github.com/statgenetics/statgen-courses/blob/master/notebooks/VAT.ipynb VAT Commands in Exercise|Exercise Commands<nowiki>[Ipython notebook]</nowiki>]
To run the exercise from docker image provided,
<pre>statgen-setup login launch --tutorial vat
</pre>
The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
