Changes
From Statistical Genetics Courses
/* Preparing Your Computer */
Starting Fall 2019 we adopt [https://www.docker.com/ docker] to run our course material . We have created various [https://hub.docker.com/u/statisticalgenetics docker repositories] with source material freely available from [https://github.com/statgenetics/statgen-courses github] for users to readily setup and reproduce our tutorials on their own computers. These docker images can also be used as production tool to run relevant software on your computer (Mac, Linux or Windows) or even a high performance computing cluster (if properly configured) for your own data analysis.
===General instructions===
* [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#alternative-to-cloud-server-use-your-own-computer Instructions to setup course tutorial environment on your computer]
* [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#option-1-launch-exercise-in-jupyterlab Instructions to run course tutorial through JupyterLab]
* [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#option-2-launch-from-command-shell Instructions to run course tutorial through command line terminal]
===Preparing Your Computer===
{| class="wikitable"
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||{{#ev:youtube|3K-sGzxsyK0|240|center|Linux}}
||{{#ev:youtube|DRCDNBlxZ-w|240|center|Mac}}
||{{#ev:youtube|sxv45NCSFMk|240|center|Windows}}
|}
===Running Exercises===
{{#ev:youtube|OgHvRVtIIog|320}}
===Tutorial specific instructions===
We use a script [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup "statgen-setup"] to start the docker based environments for these tutorials. Please refer to the previous section for instructions on the installation of this script.
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. Command "statgen-setup login" will allow you to start and login to a Linux command line environment (regardless of your current computational environment) to perform all analysis in command shells. This works for all the tutorials on this page. Additionally, some tutorials support command "statgen-setup launch" which will start a JupyterLab server to perform the analysis.
==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]
==AnnotationAnnovar complex traits==* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.pdf Functional Annotation Exercise <nowiki>[DOCXPDF]</nowiki>]
* [[Commands in Annotation Exercise|Exercise Commands]]
</pre>
==Annovar MEndelianMendelian traits==
* [http://statgen.us/files/tutorials/FunctionalAnnotation_Annovar_final.pdf Exercise <nowiki>[PDF]</nowiki>]
* [https://statgen.us/files/2017/09/commands/annovar-functional_annotation.txt Commands Part I - Functional Annotation]
==Cochran Armitage Trend Test==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Armitage_sample_size.pdf CATT Exercise <nowiki>[PDF]</nowiki>]
</pre>
==Fine-mapping (SuSiE method)==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/finemapping.docx susieR Exercise <nowiki>[DOCX]</nowiki>]
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/finemapping_answers.docx susieR Exercise Answers <nowiki>[DOCX]</nowiki>]
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/finemapping.ipynb susieR Exercise <nowiki>[Ipython notebook]</nowiki>]
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/finemapping_answers.ipynb susieR Exercise Answers <nowiki>[Ipython notebook]</nowiki>]
To run the exercise from docker image provided,
<pre>statgen-setup launch --tutorial finemap
</pre>
==GCTA==
==GWAS: Data Quality Control==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_data_QC.docx pdf Exercise <nowiki>[PDF]</nowiki>]* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PLINK_Data_QC.ipynb Exercise <nowiki>[IPython Notebook]</nowiki>]
* [[GWAS Data QC Exercise|Exercise Commands]]
To run the exercise via JupyterLab from docker image provided,
<pre>statgen-setup login launch --tutorial plink
</pre>
Alternatively, you can opt to run the exercise via command terminal from docker image provided,
<pre>statgen-setup login --tutorial plink
</pre>
==GWAS: Association Analysis Controlling for Population Substructure==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_Substructure.docx pdf Exercise <nowiki>[PDF]</nowiki>]* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PLINK_Substructure.ipynb Exercise <nowiki>[IPython Notebook]</nowiki>]
* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]
To run the exercise via JupyterLab from docker image provided,
<pre>statgen-setup login launch --tutorial plink
</pre>
Alternatively, you can opt to run the exercise via command terminal from docker image provided,
<pre>statgen-setup login --tutorial plink
</pre>
==Homozygosity Mapper==
* [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)]
</pre>
==LD clumping==
* [https://github.com/cumc/bioworkflows/blob/master/GWAS/LD_Clumping.ipynb LD Clumping Exercise <nowiki>[IPython Notebook]</nowiki>]
To run the exercise from docker image provided,
<pre>statgen-setup launch --tutorial clumping
</pre>
==MR-JTI for TWAS==
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/MR_JTI.ipynb MR-JTI Exercise <nowiki>[IPython Notebook]</nowiki>]
To run the exercise from docker image provided,
<pre>statgen-setup launch --tutorial twas
</pre>
==Pleiotropy==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy.docx pdf Pleiotropy Exercise <nowiki>[DOCXPDF]</nowiki>]* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy_answers.docx pdf Pleiotropy Answers to Questions <nowiki>[DOCXPDF]</nowiki>]
To run the exercise from docker image provided,
==Polygenic risk prediction (NPS method)==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/NPS.docx pdf PRS NPS Exercise <nowiki>[DOCX]</nowiki>]
To run the exercise from docker image provided,
==PSEQ==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PSEQ.doc pdf PSEQ Exercise <nowiki>[DOCXPDF]</nowiki>]* [[https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PSEQ.ipynb PSEQ Commands in Exercise|Exercise Commands<nowiki>[Ipython Notebook]</nowiki>]
To run the exercise from docker image provided,
<pre>statgen-setup launch --tutorial pseq
</pre>
Notice that since PSEQ exercise does not involve generating and visualizing plots, it is also fine to use a command terminal, instead of the JupyterLab server, to run this exercise and reproduce exactly what was described in the tutorial. To do so,
<pre>statgen-setup login --tutorial pseq
</pre>
==R and PLINK==
To run the exercise from docker image provided,
<pre>statgen-setup launch --tutorial plink-r-nothnagel
</pre>
to load the data-set to the JupyterLab workspace.
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==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/VAT.docx VAT Exercise <nowiki>[DOCX]</nowiki>]
* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/VAT.ipynb VAT Exercise <nowiki>[Ipython notebook]</nowiki>]
<pre>statgen-setup launch --tutorial vat
</pre>
Then follow the prompts on the terminal output to open up the JupyterLab server in your web browser. You should find the exercise notebook in the side panel, and you can click to open it.
