Changes

We have created a debian repository to make it easier to use our tutorialsStarting Fall 2019 we adopt [https://www. This repository allows you to install all required software and example data included in tutorials on your computerdocker. Using this repository will require that you have administrator access com/ docker] to a computer with Linux Systemrun our course material . If you don't We have this level of access or your computer running non-Linux systems (Windows or OS), you have two options. First, you could install the repository on a remote cloud serve, such as created various [https://wwwhub.vultrdocker.com/ VULTRu/statisticalgenetics docker repositories]. Second, you can install a Virtual Machine program (such as with source material freely available from [https://wwwgithub.virtualbox.orgcom/ VirtualBoxstatgenetics/statgen-courses github]) on your computer, for users to readily setup and then load reproduce our pre-configured virtual machine image (VM Image) into the Virtual Machinetutorials on their own computers. You These docker images can refer also be used as production tool to these online videos [[VirtualBox Installation|here]] to install VirtualBox 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.

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]

<pre>echo "deb ===Tutorial specific instructions===We use a script [trusted=yes] https://statgengithub.uscom/deb .statgenetics/" | sudo tee statgen-a courses/etcblob/aptmaster/sources.list.dsrc/statgen.listsudo add-aptsetup "statgen-repository -y ppa:webupd8team/javasudo apt-get update</pre>setup"] to start the docker based environments for these tutorials. Please refer to the previous section for instructions on the installation of this script.

We have made a video tutorial Material and instructions for specific exercise are listed in each section below (''only those using statgen-setup command are relevant to show you how our docker based tutorials''). They provide links to install the repository step by step which is available [https://www.youtube.com/watch?v=5jRJHXxkC9g&t=19s here]materials and a minimal set of commands to use for launching and running an exercise. If Command "statgen-setup login" will allow you want to install specific exercise at start and login to a Linux command line environment (regardless of your demands, please refer current computational environment) to commands listed perform all analysis in each section belowcommand 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.

==AnnotationAnnovar complex traits==* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.2019.docx pdf Functional Annotation Exercise <nowiki>[DOCXPDF]</nowiki>]

<pre>docker pull statisticalgenetics/annovarstatgen-setup login --tutorial annovar

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 MEndelianMendelian traits==

* [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]

* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/blob/filesmaster/tutorialshandout/Armitage_sample_size_revisedArmitage_sample_size.pdf CATT Exercise <nowiki>[PDF]</nowiki>]

==Epistasis (PLINK and CASSI)==Result Files* [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)==* [httphttps://github.com/statgenetics/statgen-courses/blob/master/handout/finemapping.usdocx susieR Exercise <nowiki>[DOCX]</filesnowiki>]* [https:/2016/07github.com/gatk_resultsstatgenetics/statgen-courses/blob/master/handout/finemapping_answers.tardocx susieR Exercise Answers <nowiki>[DOCX]</nowiki>]* [https://github.gz GATKcom/IGV 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 exercisefrom 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> 

* [https://drive.googlegithub.com/filestatgenetics/dstatgen-courses/0B2pJ9cgevF3sTS1DeGxYalFTN00blob/view Bam files for master/handout/Gemini.docx Gemini exercise<nowiki>[DOCX]</nowiki>]

* [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>]

====Installing Packages====To install run the exercise via JupyterLab from packagesdocker image provided, follow the configuration steps above and run the following command.

<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>

* [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>]

====Installing Packages====To install run the exercise via JupyterLab from packagesdocker image provided, follow the configuration steps above and run the following command.

<pre>sudo aptstatgen-setup launch -get install plink-tutorialplink</pre>The Alternatively, you can opt to run the exercise's via command terminal from docker image provided, <pre>statgen-setup login --tutorial plink</pre> ==Homozygosity Mapper==* [http://statgen.us/files will then be installed in the folder ''/hometutorials/Homozygosity_mapping_exercise_part_1.pdf Exercise Part I]* [http:/shared/Plink_substructure''statgen. You can run from there or copy the us/files into your user's home directory and proceed with the /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)]

* [httphttps://github.com/statgenetics/statgen-courses/blob/master/handout/MLINK.uspdf LINKAGE Exercise <nowiki>[DOCX]</filesnowiki>]  To run the exercise from docker image provided, <pre>statgen-setup login --tutorial mlink</tutorialspre> ==LD clumping==* [https:/SEQLinkage/linkage_intro_ex_berlin_2018_with_pg_numgithub.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>] '''Under Development'''  To run the exercise from docker image provided, <pre>statgen-setup login --tutorial twas</pre> ==Pleiotropy==* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy.pdf Linkage Introduction 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. 

* [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/populationblob/Popgen_exe_ansmaster/handout/PopGen.pdf docx Popgen Exercise <nowiki>[PDFDOCX]</nowiki>]* [http:// To run the exercise from docker image provided, <pre>statgen.us-setup login --tutorial popgen</files/tutorials/population/popgen_drift.q R Script for popgen_drift]pre>* [http://statgen.us/files/tutorials/population/popgen_selection.q R Script for popgen_selection]

* [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/pseqblob/PSEQ_exercise_2019master/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 Commands 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 Commands<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/statgenetics/statgen-courses/blob/filesmaster/tutorialshandout/regression_exerciseregression.pdf docx Regression Exercise <nowiki>[PDFDOCX]</nowiki>]

To install run the exercise from packagesdocker image provided, follow the configuration steps above and run the following command. <pre>statgen-setup login --tutorial regression</pre>

* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/filesblob/tutorialsmaster/rvtdthandout/rvtdt_exercise_v3RV-TDT.pdf doc Exercise <nowiki>[PDFDOC]</nowiki>]

* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/filesblob/tutorialsmaster/seqsparkhandout/slink_ex_shortSlink.pdf doc SLINK Exercise <nowiki>[PDFDOCX]</nowiki>]

To install from packages, follow the configuration steps above and run the following command. <pre>sudo aptstatgen-setup login -get install slink-tutorialslink</pre>The exercise's files will then be installed in the folder ''/home/shared/slink''. 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/vatblob/VAT_exercise_2019_1_nographsmaster/handout/VAT.pdf docx VAT Exercise <nowiki>[PDFDOCX]</nowiki>]* [[https://github.com/statgenetics/statgen-courses/blob/master/notebooks/VAT.ipynb VAT Commands in Exercise|Exercise Commands<nowiki>[Ipython notebook]</nowiki>]

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

==VAT Mendelian==* [http://statgen.us/files/tutorials/VAT_Mendelian.pdf Exercise <nowikipre>[PDF]statgen-setup launch --tutorial vat</nowikipre>]* [[VAT mendelian commands|Exercise Commands]]  To install from packages, follow the configuration steps above and run the following command.

<pre>sudo apt-get install vtools-mendelian-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.