Changes
From Statistical Genetics Courses
/* RV-TDT */
==Running Tutorials on Your Computer==
====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.
<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 for 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>]
==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> 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]. ==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> 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]. ==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> 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>[DOCX]</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]. ==Genehunter==* [http://statgen.us/files/2016tutorials/07genehunter/gatk_resultsMult_Genehunter.tar.gz GATKpdf <nowiki>[PDF]</IGV exercisenowiki>]* [[Genehunter Exercise|Exercise Commands]]
To install from packages, follow the configuration steps above and run the following command.
<pre>sudo apt-get install genabelgenehunter-tutorial</pre>The exercise's files will then be installed in the folder ''/home/shared/genabelgenehunter''. 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]]
==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]]
To run the exercise from docker image provided, <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 can be installed following [https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions]. ==Homozygosity Mapper==Installing Packages* [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==To install from packages, follow the configuration steps above * [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)] To run the following command.exercise from docker image provided, <pre>statgen-setup login --tutorial igv</pre>
==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 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].
==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>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].
==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>sudo aptstatgen-setup login -get install regression-tutorialregression</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/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]]
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].