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.
==Alohomora==
==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 and run the following command. <pre>statgen-setup login --tutorial annovar</pre>
==Annovar MEndelian==
==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==:* [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</2016pre> The "statgen-setup" script is available [https:/07/gatk_resultsgithub.tarcom/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and can be installed following [https://github.gz GATKcom/IGV 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://drive.googlegithub.com/filestatgenetics/dstatgen-courses/0B2pJ9cgevF3sTS1DeGxYalFTN00blob/view Bam files for master/handout/Gemini.docx Gemini exercise<nowiki>[DOCX]</nowiki>]
==Genehunter==
==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_Substructure_V2PLINK_Substructure.pdf docx Exercise <nowiki>[PDF]</nowiki>]
* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]
<pre>sudo aptstatgen-setup login -get install plink-tutorialplink</pre>The exercise's files will then be installed in the folder ''/home/shared/Plink_substructure''. You can run from there or copy the files into your user's home directory and proceed with the exercise.
==IGVHomozygosity Mapper== *[httpshttp://statgen.researchus/files/tutorials/Homozygosity_mapping_exercise_part_1.bcmpdf Exercise Part I]* [http://statgen.eduus/files/softwaretutorials/igv/igv-2Homozygosity_mapping_exercise_part_2.3pdf Exercise Part II]* [http://www.97homozygositymapper.jar igv.jar Software Linkorg Data Sets] ==IGV==*[https://statgengithub.research.bcmcom/statgenetics/statgen-courses/blob/master/handout/IGV.edudocx IGV exercise <nowiki>[DOCX]</filesnowiki>]* [http:/2017/09statgen.us/datafiles/igv_exercise.zip Exercise files (VCF and BAM )] To run the exercise from 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 VCF Filescan 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>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>statgen-setup login --tutorial regression</pre>
==RV-TDT==
* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/filesblob/tutorialsmaster/rvtdthandout/rvtdt_exerciseRV-TDT.pdf doc Exercise <nowiki>[PDFDOC]</nowiki>]
* [[RV-TDT|Exercise Commands]]
==SLINK==
* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/filesblob/tutorialsmaster/seqsparkhandout/slink_ex_shortSlink.pdf doc SLINK Exercise <nowiki>[PDFDOCX]</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==
==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]]