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Tutorials

7,756 bytes added, 04:23, 25 February 2020
/* RV-TDT */
==Running Tutorials on Your Computer==
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) for your own data analysis.
The VM Image is available [https://statgen.research.bcm.edu/files/images/Statgen.ova here]. The password for the student account is "LetMeIn". Feel free In this document we will focus on discussing how to change set it up and run course tutorials on your computer, using these docker images and optionally a utility script we created to whatever you likestreamline various docker commands.
To ===Pre-requisites===Software you need to install the repository on the cloud server, virtual machine, or your own computer, you need are <code>SoS</code> (a workflow system to follow these configuration steps. Please run as the root user or using the sudo commandour course utility script) and <code>docker</code>.
====Mac and Linux users====<precode>echo "deb SoS</code> requires Python 3.6+ to run. It is recommended that you install [trusted=yes] https://statgendocs.researchconda.bcm.eduio/en/latest/deb miniconda.html Miniconda] to run Python 3 if you don't have it already. Once you have Python 3 installed, simply type <code>pip install sos</" | sudo tee -a code> to install <code>SoS</etccode>, or, check out [https:/apt/sourcesvatlab.listgithub.dio/statgen.listsudo add-aptsos-repository -y ppa:webupd8teamdocs/javasudo apt-get updaterunning.html here for alternative installation methods] if you have troubles with that command. To install <code>docker</precode>from command line please follow our instructions [http://statgen.us/lab-wiki/orientation/jupyter-setup.html#install-docker here]. Alternatively Mac users can download docker app for Mac and install from a graphical interface.
Using the following command you can install all exercises on your computerFinally please download our utility script [https://raw. If you want githubusercontent.com/statgenetics/statgen-courses/master/src/statgen-setup <code>src/statgen-setup</code>] to install specific exercise at your demands, please refer <code>PATH</code> and change it to commands listed in each section belowexecutable, eg, <code>chmod +x ~/bin/statgen-setup</code> if you put it under <code>~/bin</code> which is part of your <code>PATH</code>.To verify your setup, type:
<pre> statgen-setup -h</pre>you should see some meaningful output. ====Windows users====Running these tutorials in Windows is currently not supported. Although in principle these docker images will also work in Windows, this has not yet been tested out and we are unable to provide sure instructions to setting it up. The utility script "statgen-setup" that we provide will certainly need adjustments (though minor) to work with Windows. ===Tutorial specific instructions===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 and other features provided by our utility script please read here our [https://github.com/statgenetics/statgen-courses/blob/master/README.md complete documentation to the utility script]. ==Alohomora==* [http://statgen.us/files/tutorials/seqspark/Alohomora_Exercise_revised.pdf Exercise <nowiki>[PDF]</nowiki>]* [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Data Set]* [http://gmc.mdc-berlin.de/alohomora/ Software Link]
==Annotation==
* [httphttps://statgengithub.uscom/filesstatgenetics/tutorials/functionalstatgen-annotationcourses/blob/master/handout/FunctionalAnnotation_exercise_2018v2FunctionalAnnotation.pdf docx Functional Annotation Exercise <nowiki>[PDFDOCX]</nowiki>]
* [[Commands in Annotation Exercise|Exercise Commands]]
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]
==Cochran Armitage Trend Test==
* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/blob/filesmaster/tutorialshandout/Armitage_sample_size_Berlin_1Armitage_sample_size.pdf CATT Exercise <nowiki>[PDF]</nowiki>]
==GATK and IGV==
* [http://statgen.us/files/tutorials/Variant_calling_exercices_GATK_IGV.pdf GATK/IGV Exercise <nowiki>[PDF]</nowiki>]
====Software Links====
:* [https://www.broadinstitute.org/gatk/ GATK]
:* [http://www.broadinstitute.org/igv/ IGV] ([http://statgen.us/files/software/igv.jar Download JAR file])
====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> 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].   ==GenABELFastLMM==* [httphttps://github.com/statgenetics/statgen-courses/blob/master/handout/FASTLMM.uspdf FastLMM exercise <nowiki>[PDF]</filesnowiki>] To run the exercise from docker image provided, <pre>statgen-setup login --tutorial fastlmm-gcta</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-tutorialsthese instructions]. ==GCTA==* [https:/genabel/GenABEL_with_PLINK1github.9com/statgenetics/statgen-courses/blob/master/handout/GCTA.pdf GenABEL Exercise GCTA exercise <nowiki>[PDF]</nowiki>] To run the exercise from docker image provided, <pre>statgen-setup login --tutorial fastlmm-gcta</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]. ==Gemini==* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Gemini.docx Gemini exercise <nowiki>[GeneABEL Exercise|Exercise CommandsDOCX]</nowiki>] To run the exercise from docker image provided, <pre>statgen-setup login --tutorial gemini</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].
To install from packages, follow the configuration steps above and run the following command.
<pre>sudo apt-get install genabel-tutorial</pre>
The exercise's files will then be installed in the folder ''/home/shared/genabel''. You can run from there or copy the files into your user's home directory and proceed with the exercise.
==Genehunter==
* [http://statgen.us/files/tutorials/genehunter/Mult_Genehunter.pdf <nowiki>[PDF]</nowiki>]
* [[GeneABEL 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==
* [httphttps://statgengithub.uscom/filesstatgenetics/tutorials/gwasstatgen-qccourses/blob/master/handout/PLINK_data_QC.pdf docx Exercise <nowiki>[PDF]</nowiki>]
* [[GWAS Data QC Exercise|Exercise Commands]]
====Installing Packages====To install run the exercise from packagesdocker image provided, follow the configuration steps above  <pre>statgen-setup login --tutorial plink</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]. 
<pre>sudo apt-get install plink-tutorial</pre>
The exercise's files will then be installed in the folder ''/home/shared/Plink_DataQC''. You can run from there or copy the files into your user's home directory and proceed with the exercise.
==GWAS: Association Analysis Controlling for Population Substructure==
* [httphttps://statgengithub.uscom/filesstatgenetics/tutorials/gwasstatgen-substructurecourses/blob/master/handout/GWAS_Data_Controlling_for_SubstructurePLINK_Substructure.pdf docx Exercise <nowiki>[PDF]</nowiki>]
* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]
====Installing Packages====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 plink-tutorialplink</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/Plink_substructure''statgenetics/statgen-courses/blob/master/README. You can run from there or copy md#prepare-your-computer-to-manage-the -tutorials these instructions].   ==Homozygosity Mapper==* [http://statgen.us/files into your user's home directory /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 proceed with BAM)] To run the exercisefrom docker image provided, <pre>statgen-setup login --tutorial igv</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].
==Linkage/FastLinkage==
* [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</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-tutorialsthese instructions]. ==Pleiotropy==* [https:/SEQLinkage/linkage_intro_ex_berlin_2018_with_pg_numgithub.pdf Linkage Introduction com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy.docx Pleiotropy Exercise <nowiki>[PDFDOCX]</nowiki>]* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy_answers.docx Pleiotropy Answers to Questions <nowiki>[DOCX]</nowiki>] To run the exercise from docker image provided, <pre>statgen-setup login --tutorial pleiotropy</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]. ==Polygenic risk prediction (NPS method)==* [https://github.com/statgenetics/statgen-courses/blob/master/handout/NPS.docx PRS NPS Exercise <nowiki>[DOCX]</nowiki>] To run the exercise from docker image provided, <pre>statgen-setup login --tutorial nps</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].
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==Population Genetics==
* [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 R Script for popgen_driftmaster/src/statgen-setup here]* and can be installed following [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/populationblob/popgen_selectionmaster/README.q R Script for popgen_selectionmd#prepare-your-computer-to-manage-the-tutorials these instructions].
==PSEQ==
* [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/pseqblob/PSEQ_exercisemaster/handout/PSEQ.pdf doc PSEQ Exercise <nowiki>[PDFDOCX]</nowiki>]
* [[PSEQ Commands in Exercise|Exercise Commands]]
To install run the exercise from packagesdocker image provided, follow the configuration steps above and run the following command. <pre>statgen-setup login --tutorial pseq</pre>
<pre>sudo aptThe "statgen-get install plinkseqsetup" 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/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].
==Regression==
* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/blob/filesmaster/tutorialshandout/regression_exerciseregression.pdf docx Regression Exercise <nowiki>[PDFDOCX]</nowiki>]
* [[Regression_Exercise|Exercise Commands]]
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].
==RV-TDT==
* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/filesblob/tutorialsmaster/rvtdthandout/rvtdt_exerciseRV-TDT.pdf doc Exercise <nowiki>[PDFDOC]</nowiki>]
* [[RV-TDT|Exercise Commands]]
* [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==
The exercise's files will then be installed in the folder ''/home/shared/seqspark''. You can run from there or copy the files into your user's home directory and proceed with the exercise.In order for the
commands 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>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==
* [http://statgen.us/files/tutorials/Superlink_Exercise_v2.pdf SUPERLINK Exercise <nowiki>[PDF]</nowiki>]
* [https://statgen.research.bcm.edu/files/2016/10/data/superlink.zip Superlink]
==Variant Association Tools==
* [httphttps://statgenstatgenetics.usgithub.io/filesstatgen-courses/tutorialsnotebooks/VAT_exercise_2018_nographsVAT.pdf html VAT Exercise <nowiki>[PDFHTML]</nowiki>]
* [[VAT Commands in Exercise|Exercise Commands]]
====Installing Packages====
To install from packages, follow the configuration steps above and run the following command.
To run the exercise from docker image provided, <pre>sudo aptstatgen-setup login -get install vtools-tutorialvat</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/vat''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].
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