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=yeshttps://docs.conda.io/en/latest/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</code> to install <code>SoS</code>, or, check out [https://vatlab.github.io/sos-docs/running.html here for alternative installation methods] if you have troubles with that command. To install <code>docker</code> from command line please follow our instructions [http://statgen.us/deb .lab-wiki/" | sudo tee orientation/jupyter-setup.html#install-docker here]. Alternatively Mac users can download docker app for Mac and install from a graphical interface. Finally please download our utility script [https:/etc/apt/sourcesraw.listgithubusercontent.dcom/statgenetics/statgen.listsudo add-aptcourses/master/src/statgen-repository setup <code>src/statgen-y ppa:webupd8teamsetup</javasudo aptcode>] to your <code>PATH</code> and change it to executable, eg, <code>chmod +x ~/bin/statgen-get updatesetup</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.
==Alohomora==
==Annotation==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.2019.docx Functional Annotation Exercise <nowiki>[DOCX]</nowiki>]
* [[Commands in Annotation Exercise|Exercise Commands]]
To run the exercise from docker image provided,
<pre>docker pull statisticalgenetics/annovarstatgen-setup login --tutorial annovar
</pre>
==Cochran Armitage Trend Test==
* [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> 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_V2PLINK_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]]
==Homozygosity Mapper== *[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==
* [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 exercise from docker image provided,
<pre>docker pull statisticalgenetics/igvstatgen-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].
<!--
To run the exercise from docker image provided,
<pre>docker pull statisticalgenetics/popgenstatgen-setup login --tutorial popgen
</pre>
To run the exercise from docker image provided,
<pre>docker pull statisticalgenetics/pseqstatgen-setup login --tutorial pseq
</pre>
To run the exercise from docker image provided,
<pre>docker pull statisticalgenetics/regressionstatgen-setup login --tutorial regression
</pre>
==RV-TDT==
* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/filesblob/tutorialsmaster/rvtdthandout/rvtdt_exercise_v3RV-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==
To run the exercise from docker image provided,
<pre>docker pull statisticalgenetics/vatstatgen-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].