Changes
From Statistical Genetics Courses
==Running Tutorials on Your Computer==
In this document we will focus on discussing how to set it up and run course tutorials on your computer, using these docker images and optionally a utility script we created to streamline various docker commands.
===Pre-requisites===
Software you need to install on your computer are <code>SoS</code> (a workflow system to run our course utility script) and <code>docker</code>.
====Mac and Linux users====
<code>SoS</code> requires Python 3.6+ to run. It is recommended that you install [https://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/lab-wiki/orientation/jupyter-setup.html#install-docker here]. Alternatively Mac users can download docker app for Mac and install from a graphical interface.
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===
==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]]
==Cochran Armitage Trend Test==
* [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/Armitage_sample_size_revised.pdf CATT Exercise <nowiki>[PDF]<blob/nowiki>] ==GATK and IGV==* [http:master/handout/statgen.us/files/tutorials/Variant_calling_exercices_GATK_IGVArmitage_sample_size.pdf GATK/IGV CATT 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====:* [http://statgen.us/files/2016/07/gatk_results.tar.gz GATK/IGV exercise]
==Gemini==
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==
==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]]
<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/statgenetics/statgen-courses/blob/master/Plink_substructure''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].
==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]
==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)]
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].
