Changes
From Statistical Genetics Courses
==Running Tutorials on Your Computer==
===Pre-requisitesGeneral 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]
===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. For advanced options Command "statgen-setup login" will allow you to start and other features provided by our utility script please read our [https://githublogin to a Linux command line environment (regardless of your current computational environment) to perform all analysis in command shells.com/statgenetics/This works for all the tutorials on this page. Additionally, some tutorials support command "statgen-courses/blob/master/README.md complete documentation setup launch" which will start a JupyterLab server to perform the utility script here]analysis.
==Alohomora==
* [http://gmc.mdc-berlin.de/alohomora/ Software Link]
==AnnotationAnnovar complex traits==* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.2019.docx pdf Functional Annotation Exercise <nowiki>[DOCXPDF]</nowiki>]
* [[Commands in Annotation Exercise|Exercise Commands]]
</pre>
* [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==
* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/blob/filesmaster/tutorialshandout/Armitage_sample_size_revisedArmitage_sample_size.pdf CATT Exercise <nowiki>[PDF]</nowiki>]
====Result Files==Epistasis (PLINK and CASSI)==:* [httphttps://statgengithub.uscom/filesstatgenetics/2016statgen-courses/07blob/gatk_resultsmaster/handout/Epistasis_PLINK_CASSI.tar.gz GATKpdf Epistasis exercise <nowiki>[PDF]</IGV exercisenowiki>]
To run the exercise from docker image provided, <pre>statgen-setup login --tutorial epistasis</pre> ==GeminiFastLMM==* [https://github.com/statgenetics/statgen-courses/blob/master/handout/GeminiFASTLMM.docx Gemini pdf FastLMM exercise <nowiki>[DOCXPDF]</nowiki>]
To run the exercise from docker image provided,
<pre>statgen-setup login --tutorial geminifastlmm-gcta
</pre>
==GenABELFine-mapping (SuSiE method)==* [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/blob/master/genabelhandout/GenABEL_with_PLINK1finemapping.9docx susieR Exercise <nowiki>[DOCX]</nowiki>]* [https://github.com/statgenetics/statgen-courses/blob/master/handout/finemapping_answers.pdf GenABEL docx susieR Exercise Answers <nowiki>[PDFDOCX]</nowiki>]* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/finemapping.ipynb susieR Exercise <nowiki>[GeneABEL Ipython notebook]</nowiki>]* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/finemapping_answers.ipynb susieR Exercise|Exercise CommandsAnswers <nowiki>[Ipython notebook]</nowiki>]
To run the exercise from docker image provided, <pre>sudo aptstatgen-setup launch -get install genabel-tutorialfinemap</pre>The ==GCTA==* [https://github.com/statgenetics/statgen-courses/blob/master/handout/GCTA.pdf GCTA exercise's files will then be installed in <nowiki>[PDF]</nowiki>] To run the folder ''exercise from docker image provided, <pre>statgen-setup login --tutorial fastlmm-gcta</homepre> ==Gemini==* [https:/shared/genabel''github. You can com/statgenetics/statgen-courses/blob/master/handout/Gemini.docx Gemini exercise <nowiki>[DOCX]</nowiki>] To run from there or copy the files into your user's home directory and proceed with the exercise.from docker image provided, <pre>statgen-setup login --tutorial gemini</pre>
==Genehunter==
==GWAS: Data Quality Control==
* [httphttps://statgengithub.uscom/filesstatgenetics/tutorials/gwasstatgen-qccourses/PLINK_data_QC_V2blob/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]]
<pre>sudo aptstatgen-setup launch -get install plink-tutorialplink</pre>The exercise's files will then be installed in the folder ''/home/shared/Plink_DataQC''. You Alternatively, you can opt to run from there or copy the files into your user's home directory and proceed with the exercise.via command terminal from docker image provided, <pre>statgen-setup login --tutorial plink</pre>
==GWAS: Association Analysis Controlling for Population Substructure==
* [httphttps://statgengithub.uscom/filesstatgenetics/tutorials/gwasstatgen-substructurecourses/GWAS_Data_Controlling_for_Substructure_V2blob/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]]
<pre>sudo aptstatgen-setup launch -get install plink-tutorialplink</pre>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.
<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]
==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==
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</pre>
==PSEQ==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PSEQ.doc pdf PSEQ Exercise <nowiki>[DOCXPDF]</nowiki>]* [[https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PSEQ.ipynb PSEQ Commands in Exercise|Exercise Commands<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>
==Regression==
</pre>
==RV-TDT==
* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/filesblob/tutorialsmaster/rvtdthandout/rvtdt_exercise_v3RV-TDT.pdf doc Exercise <nowiki>[PDFDOC]</nowiki>]
* [[RV-TDT|Exercise Commands]]
To run the exercise from docker image provided,
<pre>statgen-setup login --tutorial slink</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].
==SUPERLINK==
==Variant Association Tools==
* [https://statgenetics.github.iocom/statgenetics/statgen-courses/notebooksblob/master/handout/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>