Changes

We have created a debian repository to make it easier to use our tutorials. This repository allows you to install all required software and example data included in tutorials on your computer. Using this repository will require that you have administrator access to a computer with Linux System. If you don't 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 [https://www.vultr.com/ VULTR]. Second, you can install a Virtual Machine program (such as [https://www.virtualbox.org/ VirtualBox]) on your computer, and then load our pre-configured virtual machine image (VM Image) into the Virtual Machine. You can refer to these online videos [[VirtualBox Installation|here]] to install VirtualBox on your computer.

<pre>echo "deb [trusted=yes] https://statgen.research.bcm.eduus/deb ./" | sudo tee -a /etc/apt/sources.list.d/statgen.list

Using the following command We have made a video tutorial to show you can how to install all exercises on your computerthe repository step by step which is available [https://www.youtube.com/watch?v=5jRJHXxkC9g&t=19s here]. If you want to install specific exercise at your demands, please refer to commands listed in each section below.

==Alohomora==* [http://statgen.us/files/tutorials/seqspark/Alohomora_Exercise_revised.pdf Exercise <prenowiki> [PDF]</prenowiki>]* [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Data Set]* [http://gmc.mdc-berlin.de/alohomora/ Software Link]

* [httphttps://statgengithub.us/filescom/tutorialsstatgenetics/functionalstatgen-annotationcourses/FunctionalAnnotation_exercise_2018v2blob/master/handout/FunctionalAnnotation.2019.pdf docx Functional Annotation Exercise <nowiki>[PDFDOCX]</nowiki>]* [[Commands in Annotation Exercise|Exercise Commands in Exercise]]

To install run the exercise from packagesdocker image provided, follow the configuration steps above  <pre>statgen-setup login --tutorial annovar</pre> The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and run the can be installed following command[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 <prenowiki>sudo apt-get install annotation-tutorial[PDF]</prenowiki>]The exercise's * [https://statgen.research.bcm.edu/files will then be installed in the folder ''/home2017/shared09/commands/annovar-functional_annotation''. You can run from there or copy the txt Commands Part I - Functional Annotation]* [https://statgen.research.bcm.edu/files into your user's home directory and proceed with the exercise/2017/09/commands/annovar-variant_filtering.txt Commands Part II - Variant Filtering]

* [http://statgen.us/files/tutorials/Armitage_sample_size_Berlin_1Armitage_sample_size_revised.pdf CATT Exercise <nowiki>[PDF]</nowiki>]

* [[GeneABEL Exercise|Commands in ExerciseCommands]]

* [http://statgen.us/files/tutorials/gwas-qc/PLINK_data_QCPLINK_data_QC_V2.pdf Exercise <nowiki>[PDF]</nowiki>]* [[GWAS Data QC Exercise|Commands in ExerciseCommands]]

* [http://statgen.us/files/tutorials/gwas-substructure/GWAS_Data_Controlling_for_SubstructureGWAS_Data_Controlling_for_Substructure_V2.pdf Exercise <nowiki>[PDF]</nowiki>]* [[GWAS_Controlling_for_Population_Substructure|Commands in ExerciseCommands]]

* [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/populationblob/Popgen_exe_ansmaster/handout/PopGen.pdf docx Popgen Exercise <nowiki>[PDFDOCX]</nowiki>]*  To run the exercise from docker image provided, <pre>statgen-setup login --tutorial popgen</pre> The "statgen-setup" script is available [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/populationblob/popgen_drift.q Commands for popgen_driftmaster/src/statgen-setup here]* and can be installed following [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/populationblob/popgen_selectionmaster/README.q Commands for popgen_selectionmd#prepare-your-computer-to-manage-the-tutorials these instructions].

* [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/pseqblob/PSEQ_exercisemaster/handout/PSEQ.pdf doc PSEQ Exercise <nowiki>[PDFDOCX]</nowiki>]* [[PSEQ Commands in Exercise|Exercise Commands in Exercise]]

To install run the exercise from packagesdocker image provided, follow the configuration steps above and run the following command.

<pre>sudo aptstatgen-setup login -get install plinkseq-tutorialpseq</pre> The exercise's files will then "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed in the folder ''following [https:/home/sharedgithub.com/pseq''statgenetics/statgen-courses/blob/master/README. You can run from there or copy the files into md#prepare-your user's home directory and proceed with -computer-to-manage-the exercise-tutorials these instructions].

* [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/blob/master/handout/regression_exerciseregression.pdf docx Regression Exercise <nowiki>[PDFDOCX]</nowiki>]* [[Regression_Exercise|Commands in ExerciseCommands]]

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>

<pre>sudo aptThe "statgen-get install regressionsetup" script is available [https://github.com/statgenetics/statgen-tutorial<courses/pre>The exercise's files will then blob/master/src/statgen-setup here] and can be installed in the folder ''following [https:/home/sharedgithub.com/regression''statgenetics/statgen-courses/blob/master/README. You can run from there or copy the files into md#prepare-your user's home directory and proceed with -computer-to-manage-the exercise-tutorials these instructions].

* [http://statgen.us/files/tutorials/rvtdt/rvtdt_exerciservtdt_exercise_v3.pdf Exercise <nowiki>[PDF]</nowiki>]* [[RV-TDT|Commands in ExerciseCommands]]

* [[SEQLinkage_Commands_in_Exercise|Commands in ExerciseCommands]]

* [[SEQSpark|Commands in ExerciseCommands]]

* [https://statgenetics.github.io/statgen-courses/notebooks/VAT.html VAT Exercise <nowiki>[HTML]</nowiki>]* [[VAT Commands in Exercise|Exercise Commands]]  To run the exercise from docker image provided, <pre>statgen-setup login --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]. ==VAT Mendelian==* [http://statgen.us/files/tutorials/VAT_exercise_2018_nographsVAT_Mendelian.pdf VAT Exercise <nowiki>[PDF]</nowiki>]* [[VAT Commands in Exercisemendelian commands|Commands in ExerciseCommands]] 

<pre>sudo apt-get install vtools-mendelian-tutorial</pre>