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Tutorials

13,374 bytes added, 16:06, 8 November 2022
/* Preparing Your Computer */
==Running Tutorials on Your Computer==
Starting Fall 2019 we adopt [https://www.docker.com/ docker] to run our course material . We have created a debian repository to make it easier 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 use readily setup and reproduce our tutorialson their own computers. Using this repository will require that you have administrator access These docker images can also be used as production tool to the computer run relevant software on which you'll be using them. If you don't have this level of accessyour computer (Mac, we also provide Linux or Windows) or even a pre-high performance computing cluster (if properly configured virtual machine image that will allow you to install software as root) for your own data analysis.
The VM Image is available ===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.research.bcm.educom/filesstatgenetics/imagesstatgen-courses/Statgenwiki/How-to-launch-course-tutorials#option-1-launch-exercise-in-jupyterlab Instructions to run course tutorial through JupyterLab]* [https://github.ova herecom/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#option-2-launch-from-command-shell Instructions to run course tutorial through command line terminal]
If you would like to ===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 our repository on VM or on your computer, follow a script [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup "statgen-setup"] to start the docker based environments for these configuration stepstutorials. Please run as refer to the root user or using previous section for instructions on the sudo commandinstallation of this script.<pre>addMaterial and instructions for specific exercise are listed in each section below (''only those using statgen-aptsetup 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-repository ppasetup 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:webupd8team/javaecho "deb /statgen.us/files/tutorials/Alohomora_Exercise_revised.pdf Exercise <nowiki>[trusted=yesPDF] </nowiki>]* [https://statgen.research.bcm.edu/deb .files/" > 2016/etc10/aptdata/sourcesalohomora.listzip Data Set]* [http://gmc.dmdc-berlin.de/alohomora/ Software Link] ==Annovar complex traits==* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.listpdf Functional Annotation Exercise <nowiki>[PDF]</nowiki>]apt* [[Commands in Annotation Exercise|Exercise Commands]] To run the exercise from docker image provided, <pre>statgen-setup login --get updatetutorial 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==
* [http://statgen.us/files/tutorials/population/berlinseq.2.2.PopGen_exercise.pdf Population Exercise <nowiki>[PDF]</nowiki>]
* [http://statgen.us/files/tutorials/population/berlinseq.2.2.PopGen_answers.pdf Exercise Answers <nowiki>[PDF]</nowiki>]
* [http://statgen.us/files/tutorials/population/popgen_drift.q Commands for popgen_drift]
* [http://statgen.us/files/tutorials/population/popgen_selection.q Commands for popgen_selection]
-->
==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==
* [httpshttp://statgen.research.bcm.eduus/files/tutorials/seqspark/SEQSpark_exercise_Final_v3SEQSpark_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.
To <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 packages, folow there or copy the configuration steps above files into your user's home directory and run proceed with the following exercise.In order for thecommands as an root on your 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>aptstatgen-get install oraclesetup login -java8-installer hadoop seqspark-tutorialslink</pre>The exercise's ==SUPERLINK==* [http://statgen.us/files will then be installed in /hometutorials/Superlink_Exercise_v2.pdf SUPERLINK Exercise <nowiki>[PDF]</nowiki>]* [https:/shared/seqsparkstatgen. You can run from there or copy the research.bcm.edu/files into your user's home directory and proceed with the exercise/2016/10/data/superlink.zip Superlink]
==Variant Association Tools==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/VAT.researchdocx VAT Exercise <nowiki>[DOCX]</nowiki>]* [https://github.bcm.educom/filesstatgenetics/tutorialsstatgen-courses/vatblob/VAT_exercise_2018%20with_graphsmaster/notebooks/VAT.pdf ipynb VAT Exercise <nowiki>[PDFIpython 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.
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