Changes
From Statistical Genetics Courses
/* LD clumping */
===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]
===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://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>[PDF]</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.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 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.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>] '''Under Development'''
To run the exercise from docker image provided,
<pre>statgen-setup login --tutorial twas
</pre>
==Pleiotropy==
==PSEQ==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PSEQ.pdf PSEQ Exercise <nowiki>[PDF]</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 login 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>
==REGENIE==
to load the data-set to the JupyterLab workspace.
