Changes

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://statgengithub.research.bcm.educom/filesstatgenetics/imagesstatgen-courses/Statgen.ova herewiki/How-to-launch-course-tutorials#alternative-to-cloud-server-use-your-own-computer Instructions to setup course tutorial environment on your computer]* [https://github. The password for the student account is "LetMeIn". Feel free com/statgenetics/statgen-courses/wiki/How-to change it -launch-course-tutorials#option-1-launch-exercise-in-jupyterlab Instructions to whatever you likerun 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]

===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 <prenowiki>echo "deb [trusted=yesPDF] </nowiki>]* [https://statgen.research.bcm.edu/deb files/2016/10/data/alohomora.zip Data Set]* [http:/" | sudo tee /gmc.mdc-a berlin.de/etcalohomora/aptSoftware Link] ==Annovar complex traits==* [https:/sources.list/github.dcom/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.listpdf Functional Annotation Exercise <nowiki>[PDF]</nowiki>]sudo add* [[Commands in Annotation Exercise|Exercise Commands]] To run the exercise from docker image provided, <pre>statgen-aptsetup login -repository ppa:webupd8team/javasudo apt-get updatetutorial annovar

==AnnotationAnnovar Mendelian traits==* [http://statgen.us/files/tutorials/functional-annotation/FunctionalAnnotation_exercise_2018v2FunctionalAnnotation_Annovar_final.pdf Functional Annotation 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]

* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/blob/filesmaster/tutorialshandout/Armitage_sample_size_Berlin_1Armitage_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>  ==GenABELFastLMM==* [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/genabelgenehunter/GenABEL_with_PLINK1.9Mult_Genehunter.pdf GenABEL Exercise <nowiki>[PDF]</nowiki>]* [[GeneABEL Genehunter Exercise|Commands in ExerciseCommands]]

<pre>sudo apt-get install plinkgenehunter-tutorial</pre>The exercise's files will then be installed in the folder ''/home/shared/Plink_DataQCgenehunter''. 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>

* [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/gwasHomozygosity_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-substructurecourses/GWAS_Data_Controlling_for_Substructureblob/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.

* [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/blob/master/handout/regression_exerciseregression.pdf docx Regression Exercise <nowiki>[PDFDOCX]</nowiki>]* [[Regression_Exercise|Commands in ExerciseCommands]] To run the exercise from docker image provided, <pre>statgen-setup login --tutorial regression</pre> 

* [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/rvtdtblob/rvtdt_exercisemaster/handout/RV-TDT.pdf doc Exercise <nowiki>[PDFDOC]</nowiki>]* [[RV-TDT|Exercise Commands]]

==Population GeneticsSEQLinkage==* [http://statgen.us/files/tutorials/populationSEQLinkage/Popgen_exe_ansSEQLinkage_revised_with_pg_numb.pdf Popgen SEQLinkage Exercise <nowiki>[PDF]</nowiki>]* [http://statgen.us/files/tutorials/population/popgen_drift.q [SEQLinkage_Commands_in_Exercise|Exercise Commands for popgen_drift]* [http://statgen.us/files/tutorials/population/popgen_selection.q Commands for popgen_selection]

==PSEQ==* [http://statgenTo install from packages, follow the configuration steps above and run the following command.us/files/tutorials/pseq/PSEQ_exercise.pdf PSEQ Exercise  <nowikipre>[PDF]sudo apt-get install seqlinkage-tutorial</nowikipre>]* [[PSEQ Commands The exercise's files will then be installed in Exercise|Commands in Exercise]]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.

* [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/VAT_exercise_2018_nographsblob/master/handout/VAT.pdf docx VAT Exercise <nowiki>[PDFDOCX]</nowiki>]* [[https://github.com/statgenetics/statgen-courses/blob/master/notebooks/VAT.ipynb VAT Commands in Exercise|Commands in Exercise<nowiki>[Ipython notebook]</nowiki>]====Installing Packages==== To install from packages, follow the configuration steps above and run the following command.exercise from docker image provided, <pre>statgen-setup launch --tutorial vat</pre>

<pre>sudo apt-get install vtools-tutorial</pre>The exercise's files will then be installed in Then follow the folder ''/home/shared/vat''prompts on the terminal output to open up the JupyterLab server in your web browser. You can run from there or copy the files into your user's home directory and proceed with should find the exercisenotebook in the side panel, and you can click to open it.