Difference between revisions of "Tutorials"

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	==Running Tutorials on Your Computer==		==Running Tutorials on Your Computer==
−	We have created a debian repository to make it easier to use our tutorials. This repository allows you to install all required software and example data included in tutorials on your computer. Using this repository will require that you have administrator access to a computer with Linux System. If you don't have this level of access or your computer running non-Linux systems (Windows or OS), you have two options. First, you could install the repository on a remote cloud serve, such as [https://www.vultr.com/ VULTR]. Second, you can install a Virtual Machine program (such as [https://www.virtualbox.org/ VirtualBox]) on your computer, and then load our pre-configured virtual machine image (VM Image) into the Virtual Machine. You can refer to these online videos [[VirtualBox Installation|here]] to install VirtualBox on 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.
−	The VM Image is available [https://statgen.research.bcm.edu/files/images/Statgen.ova here]. The password for the student account is "LetMeIn". Feel free to change it to whatever you like.	+	===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]
−	To install the repository on the cloud server, virtual machine, or your own computer, you need to follow these configuration steps. Please run as the root user or using the sudo command.	+	===Preparing Your Computer===
		+	{| class="wikitable"
		+	|-
		+	||{{#ev:youtube|3K-sGzxsyK0|240|center|Linux}}
		+	||{{#ev:youtube|DRCDNBlxZ-w|240|center|Mac}}
		+	||{{#ev:youtube|sxv45NCSFMk|240|center|Windows}}
		+	|}
−	<pre>echo "deb [trusted=yes] https://statgen.research.bcm.edu/deb ./" | sudo tee -a /etc/apt/sources.list.d/statgen.list	+	===Running Exercises===
−	sudo add-apt-repository -y ppa:webupd8team/java	+	{{#ev:youtube|OgHvRVtIIog|320}}
−	sudo apt-get update	+
−	</pre>	+
−	We have made a video tutorial to show you how to install the repository step by step which is available [https://www.youtube.com/watch?v=5jRJHXxkC9g&t=19s here]. If you want to install specific exercise at your demands, please refer to commands listed in each section below.	+	===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==		==Alohomora==
−	* [http://statgen.us/files/tutorials/seqspark/Alohomora_Exercise_revised.pdf Exercise <nowiki>[PDF]</nowiki>]	+	* [http://statgen.us/files/tutorials/Alohomora_Exercise_revised.pdf Exercise <nowiki>[PDF]</nowiki>]
	* [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Data Set]		* [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Data Set]
	* [http://gmc.mdc-berlin.de/alohomora/ Software Link]		* [http://gmc.mdc-berlin.de/alohomora/ Software Link]
−	==Annotation==	+	==Annovar complex traits==
−	* [http://statgen.us/files/tutorials/functional-annotation/FunctionalAnnotation_exercise_2018v2.pdf Functional Annotation Exercise <nowiki>[PDF]</nowiki>]	+	* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.pdf Functional Annotation Exercise <nowiki>[PDF]</nowiki>]
	* [[Commands in Annotation Exercise|Exercise Commands]]		* [[Commands in Annotation Exercise|Exercise Commands]]
−	To install from packages, follow the configuration steps above and run the following command.	+	To run the exercise from docker image provided,
−	<pre>sudo apt-get install annotation-tutorial</pre>	+	<pre>statgen-setup login --tutorial annovar
−	The exercise's files will then be installed in the folder ''/home/shared/functional_annotation''. You can run from there or copy the files into your user's home directory and proceed with the exercise.	+	</pre>
−	==Annovar MEndelian==	+	==Annovar Mendelian traits==
	* [http://statgen.us/files/tutorials/FunctionalAnnotation_Annovar_final.pdf Exercise <nowiki>[PDF]</nowiki>]		* [http://statgen.us/files/tutorials/FunctionalAnnotation_Annovar_final.pdf Exercise <nowiki>[PDF]</nowiki>]
−	* [https://statgen.research.bcm.edu/files/2017/09/commands/annovar-functional_annotation.txt Commands Part I - Functional Annotation]	+	* [https://statgen.us/files/2017/09/commands/annovar-functional_annotation.txt Commands Part I - Functional Annotation]
−	* [https://statgen.research.bcm.edu/files/2017/09/commands/annovar-variant_filtering.txt Commands Part II - Variant Filtering]	+	* [https://statgen.us/files/2017/09/commands/annovar-variant_filtering.txt Commands Part II - Variant Filtering]
	==Cochran Armitage Trend Test==		==Cochran Armitage Trend Test==
−	* [http://statgen.us/files/tutorials/Armitage_sample_size_Berlin_1.pdf CATT Exercise <nowiki>[PDF]</nowiki>]	+	* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Armitage_sample_size.pdf CATT Exercise <nowiki>[PDF]</nowiki>]
−	==GATK and IGV==
−	* [http://statgen.us/files/tutorials/Variant_calling_exercices_GATK_IGV.pdf GATK/IGV 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====	+	==Epistasis (PLINK and CASSI)==
−	:* [http://statgen.us/files/2016/07/gatk_results.tar.gz GATK/IGV exercise]	+	* [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>
		+
		+
		+	==FastLMM==
		+	* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FASTLMM.pdf FastLMM exercise <nowiki>[PDF]</nowiki>]
		+
		+	To run the exercise from docker image provided,
		+
		+	<pre>statgen-setup login --tutorial fastlmm-gcta
		+	</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==
		+	* [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>
		+
	==Gemini==		==Gemini==
−	* [https://drive.google.com/file/d/0B2pJ9cgevF3sTS1DeGxYalFTN00/view Bam files for exercise]	+	* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Gemini.docx Gemini exercise <nowiki>[DOCX]</nowiki>]
−	==GenABEL==	+	To run the exercise from docker image provided,
−	* [http://statgen.us/files/tutorials/genabel/GenABEL_with_PLINK1.9.pdf GenABEL Exercise <nowiki>[PDF]</nowiki>]	+
−	* [[GeneABEL Exercise|Exercise Commands]]	+
−	To install from packages, follow the configuration steps above and run the following command.	+	<pre>statgen-setup login --tutorial gemini
		+	</pre>
−	<pre>sudo apt-get install genabel-tutorial</pre>
−	The exercise's files will then be installed in the folder ''/home/shared/genabel''. You can run from there or copy the files into your user's home directory and proceed with the exercise.
	==Genehunter==		==Genehunter==
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	==GWAS: Data Quality Control==		==GWAS: Data Quality Control==
−	* [http://statgen.us/files/tutorials/gwas-qc/PLINK_data_QC.pdf Exercise <nowiki>[PDF]</nowiki>]	+	* [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]]		* [[GWAS Data QC Exercise|Exercise Commands]]
−	====Installing Packages====	+	To run the exercise via JupyterLab from docker image provided,
−	To install from packages, follow the configuration steps above and run the following command.	+
−	<pre>sudo apt-get install plink-tutorial</pre>	+	<pre>statgen-setup launch --tutorial plink
−	The exercise's files will then be installed in the folder ''/home/shared/Plink_DataQC''. You can run from there or copy the files into your user's home directory and proceed with the exercise.	+	</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==		==GWAS: Association Analysis Controlling for Population Substructure==
−	* [http://statgen.us/files/tutorials/gwas-substructure/GWAS_Data_Controlling_for_Substructure.pdf Exercise <nowiki>[PDF]</nowiki>]	+	* [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]]		* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]
−	====Installing Packages====	+	To run the exercise via JupyterLab from docker image provided,
−	To install from packages, follow the configuration steps above and run the following command.	+
−	<pre>sudo apt-get install plink-tutorial</pre>	+	<pre>statgen-setup launch --tutorial plink
−	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.	+	</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==
		+	* [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)]
−	==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://statgen.research.bcm.edu/files/software/igv/igv-2.3.97.jar igv.jar Software Link]
−	*[https://statgen.research.bcm.edu/files/2017/09/data/igv_exercise.zip BAM and VCF Files]
	==Linkage/FastLinkage==		==Linkage/FastLinkage==
−	* [http://statgen.us/files/tutorials/SEQLinkage/linkage_intro_ex_berlin_2018_with_pg_num.pdf Linkage Introduction <nowiki>[PDF]</nowiki>]	+	* [https://github.com/statgenetics/statgen-courses/blob/master/handout/MLINK.pdf LINKAGE Exercise <nowiki>[DOCX]</nowiki>]
		+
		+
		+	To run the exercise from docker image provided,
		+
		+	<pre>statgen-setup login --tutorial mlink
		+	</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.pdf Pleiotropy Exercise <nowiki>[PDF]</nowiki>]
		+	* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy_answers.pdf Pleiotropy Answers to Questions <nowiki>[PDF]</nowiki>]
		+
		+	To run the exercise from docker image provided,
		+
		+	<pre>statgen-setup login --tutorial pleiotropy
		+	</pre>
		+
		+
		+	==Polygenic risk prediction (NPS method)==
		+	* [https://github.com/statgenetics/statgen-courses/blob/master/handout/NPS.pdf PRS NPS Exercise <nowiki>[DOCX]</nowiki>]
		+
		+	To run the exercise from docker image provided,
		+
		+	<pre>statgen-setup login --tutorial nps
		+	</pre>
		+
		+
		+	==Polygenic risk prediction (LDpred2 method)==
		+	* [https://github.com/statgenetics/statgen-courses/blob/master/handout/ldpred2_example.pdf PRS LDpred2 Exercise <nowiki>[PDF]</nowiki>]
		+	* [https://github.com/cumc/bioworkflows/blob/master/ldpred/ldpred2_example.ipynb PRS LDpred2 Exercise <nowiki>[Ipython Notebook]</nowiki>]
		+
		+
		+	To run the exercise from docker image provided,
		+
		+	<pre>statgen-setup launch --tutorial ldpred2
		+	</pre>
		+
		+	Then follow prompts on the terminal output to open up the JupyterLab server in your web browser. If it is the first time you start this server, please open a command terminal inside JupyterLab, and type
		+
		+	<pre>get-data</pre>
		+
		+	to load the data-set to the JupyterLab workspace.
		+
	<!--		<!--
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	-->		-->
	==Population Genetics==		==Population Genetics==
−	* [http://statgen.us/files/tutorials/population/Popgen_exe_ans.pdf Popgen Exercise <nowiki>[PDF]</nowiki>]	+	* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PopGen.docx Popgen Exercise <nowiki>[DOCX]</nowiki>]
−	* [http://statgen.us/files/tutorials/population/popgen_drift.q R Script for popgen_drift]	+
−	* [http://statgen.us/files/tutorials/population/popgen_selection.q R Script for popgen_selection]	+
		+	To run the exercise from docker image provided,
		+
		+	<pre>statgen-setup login --tutorial popgen
		+	</pre>
		+
	==PSEQ==		==PSEQ==
−	* [http://statgen.us/files/tutorials/pseq/PSEQ_exercise.pdf PSEQ Exercise <nowiki>[PDF]</nowiki>]	+	* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PSEQ.pdf PSEQ Exercise <nowiki>[PDF]</nowiki>]
−	* [[PSEQ Commands in Exercise|Exercise Commands]]	+	* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PSEQ.ipynb PSEQ Exercise <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>
		+
		+
		+	==REGENIE==
		+	* [https://github.com/statgenetics/statgen-courses/blob/master/handout/regenie_example.pdf REGENIE Exercise <nowiki>[PDF]</nowiki>]
		+	* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/regenie_example.ipynb REGENIE Exercise <nowiki>[Ipython Notebook]</nowiki>]
		+
		+
		+	To run the exercise from docker image provided,
		+
		+	<pre>statgen-setup launch --tutorial regenie
		+	</pre>
		+
		+	Then follow prompts on the terminal output to open up the JupyterLab server in your web browser. If it is the first time you start this server, please open a command terminal inside JupyterLab, and type
		+
		+	<pre>get-data</pre>
		+
		+	to load the data-set to the JupyterLab workspace.
−	To install from packages, follow the configuration steps above and run the following command.
−	<pre>sudo apt-get install plinkseq-tutorial</pre>
−	The exercise's files will then be installed in the folder ''/home/shared/pseq''. You can run from there or copy the files into your user's home directory and proceed with the exercise.
	==Regression==		==Regression==
−	* [http://statgen.us/files/tutorials/regression_exercise.pdf Regression Exercise <nowiki>[PDF]</nowiki>]	+	* [https://github.com/statgenetics/statgen-courses/blob/master/handout/regression.docx Regression Exercise <nowiki>[DOCX]</nowiki>]
	* [[Regression_Exercise|Exercise Commands]]		* [[Regression_Exercise|Exercise Commands]]
−	To install from packages, follow the configuration steps above and run the following command.	+	To run the exercise from docker image provided,
		+
		+	<pre>statgen-setup login --tutorial regression
		+	</pre>
−	<pre>sudo apt-get install regression-tutorial</pre>
−	The exercise's files will then be installed in the folder ''/home/shared/regression''. You can run from there or copy the files into your user's home directory and proceed with the exercise.
	==RV-TDT==		==RV-TDT==
−	* [http://statgen.us/files/tutorials/rvtdt/rvtdt_exercise.pdf Exercise <nowiki>[PDF]</nowiki>]	+	* [https://github.com/statgenetics/statgen-courses/blob/master/handout/RV-TDT.doc Exercise <nowiki>[DOC]</nowiki>]
	* [[RV-TDT|Exercise Commands]]		* [[RV-TDT|Exercise Commands]]
Line 142:		Line 291:
	* [http://statgen.us/files/tutorials/SEQLinkage/SEQLinkage_revised_with_pg_numb.pdf SEQLinkage Exercise <nowiki>[PDF]</nowiki>]		* [http://statgen.us/files/tutorials/SEQLinkage/SEQLinkage_revised_with_pg_numb.pdf SEQLinkage Exercise <nowiki>[PDF]</nowiki>]
	* [[SEQLinkage_Commands_in_Exercise|Exercise Commands]]		* [[SEQLinkage_Commands_in_Exercise|Exercise Commands]]
		+
		+
		+	To install from packages, follow the configuration steps above and run the following command.
		+
		+	<pre>sudo apt-get install seqlinkage-tutorial</pre>
		+	The exercise's files will then be installed in the folder ''/home/shared/seqlinkage''. You can run from there or copy the files into your user's home directory and proceed with the exercise.
	==SEQSpark==		==SEQSpark==
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	==SLINK==		==SLINK==
−	* [http://statgen.us/files/tutorials/seqspark/slink_ex_short.pdf SLINK Exercise <nowiki>[PDF]</nowiki>]	+	* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Slink.doc SLINK Exercise <nowiki>[DOCX]</nowiki>]
		+
		+	To run the exercise from docker image provided,
		+
		+	<pre>statgen-setup login --tutorial slink</pre>
	==SUPERLINK==		==SUPERLINK==
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	==Variant Association Tools==		==Variant Association Tools==
−	* [http://statgen.us/files/tutorials/VAT_exercise_2018_nographs.pdf VAT Exercise <nowiki>[PDF]</nowiki>]	+	* [https://github.com/statgenetics/statgen-courses/blob/master/handout/VAT.docx VAT Exercise <nowiki>[DOCX]</nowiki>]
−	* [[VAT Commands in Exercise|Exercise Commands]]	+	* [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/VAT.ipynb VAT Exercise <nowiki>[Ipython notebook]</nowiki>]
−	====Installing Packages====
−	To install from packages, follow the configuration steps above and run the following command.
−	<pre>sudo apt-get install vtools-tutorial</pre>	+	To run the exercise from docker image provided,
−	The exercise's files will then be installed in the folder ''/home/shared/vat''. You can run from there or copy the files into your user's home directory and proceed with the exercise.	+
		+	<pre>statgen-setup launch --tutorial vat
		+	</pre>
−	==VAT Mendelian==	+	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.
−	* [http://statgen.us/files/tutorials/VAT_Mendelian.pdf Exercise <nowiki>[PDF]</nowiki>]	+
−	* [[VAT mendelian commands|Exercise Commands]]	+

---

Latest revision as of 16:06, 8 November 2022

Running Tutorials on Your Computer

Starting Fall 2019 we adopt docker to run our course material . We have created various docker repositories with source material freely available from 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

• Instructions to setup course tutorial environment on your computer
• Instructions to run course tutorial through JupyterLab
• Instructions to run course tutorial through command line terminal

Preparing Your Computer

Linux

Mac

Windows

Running Exercises

Tutorial specific instructions

We use a script "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

• Exercise [PDF]
• Data Set
• Software Link

Annovar complex traits

• Functional Annotation Exercise [PDF]
• Exercise Commands

To run the exercise from docker image provided,

statgen-setup login --tutorial annovar

Annovar Mendelian traits

• Exercise [PDF]
• Commands Part I - Functional Annotation
• Commands Part II - Variant Filtering

Cochran Armitage Trend Test

• CATT Exercise [PDF]

Epistasis (PLINK and CASSI)

• Epistasis exercise [PDF]

To run the exercise from docker image provided,

statgen-setup login --tutorial epistasis

FastLMM

• FastLMM exercise [PDF]

To run the exercise from docker image provided,

statgen-setup login --tutorial fastlmm-gcta

Fine-mapping (SuSiE method)

• susieR Exercise [DOCX]
• susieR Exercise Answers [DOCX]
• susieR Exercise [Ipython notebook]
• susieR Exercise Answers [Ipython notebook]

To run the exercise from docker image provided,

statgen-setup launch --tutorial finemap

GCTA

• GCTA exercise [PDF]

To run the exercise from docker image provided,

statgen-setup login --tutorial fastlmm-gcta

Gemini

• Gemini exercise [DOCX]

To run the exercise from docker image provided,

statgen-setup login --tutorial gemini

Genehunter

• [PDF]
• Exercise Commands

To install from packages, follow the configuration steps above and run the following command.

sudo apt-get install genehunter-tutorial

The exercise's files will then be installed in the folder /home/shared/genehunter. You can run from there or copy the files into your user's home directory and proceed with the exercise.

GWAS: Data Quality Control

• Exercise [PDF]
• Exercise [IPython Notebook]
• Exercise Commands

To run the exercise via JupyterLab from docker image provided,

statgen-setup launch --tutorial plink

Alternatively, you can opt to run the exercise via command terminal from docker image provided,

statgen-setup login --tutorial plink

GWAS: Association Analysis Controlling for Population Substructure

• Exercise [PDF]
• Exercise [IPython Notebook]
• Exercise Commands

To run the exercise via JupyterLab from docker image provided,

statgen-setup launch --tutorial plink

Alternatively, you can opt to run the exercise via command terminal from docker image provided,

statgen-setup login --tutorial plink

Homozygosity Mapper

• Exercise Part I
• Exercise Part II
• Data Sets

IGV

• IGV exercise [DOCX]
• Exercise files (VCF and BAM)

Linkage/FastLinkage

• LINKAGE Exercise [DOCX]

To run the exercise from docker image provided,

statgen-setup login --tutorial mlink

LD clumping

• LD Clumping Exercise [IPython Notebook]

To run the exercise from docker image provided,

statgen-setup launch --tutorial clumping

MR-JTI for TWAS

• MR-JTI Exercise [IPython Notebook]

To run the exercise from docker image provided,

statgen-setup launch --tutorial twas

Pleiotropy

• Pleiotropy Exercise [PDF]
• Pleiotropy Answers to Questions [PDF]

To run the exercise from docker image provided,

statgen-setup login --tutorial pleiotropy

Polygenic risk prediction (NPS method)

• PRS NPS Exercise [DOCX]

To run the exercise from docker image provided,

statgen-setup login --tutorial nps

Polygenic risk prediction (LDpred2 method)

• PRS LDpred2 Exercise [PDF]
• PRS LDpred2 Exercise [Ipython Notebook]

To run the exercise from docker image provided,

statgen-setup launch --tutorial ldpred2

Then follow prompts on the terminal output to open up the JupyterLab server in your web browser. If it is the first time you start this server, please open a command terminal inside JupyterLab, and type

get-data

to load the data-set to the JupyterLab workspace.

Population Genetics

• Popgen Exercise [DOCX]

To run the exercise from docker image provided,

statgen-setup login --tutorial popgen

PSEQ

• PSEQ Exercise [PDF]
• PSEQ Exercise [Ipython Notebook]

To run the exercise from docker image provided,

statgen-setup launch --tutorial pseq

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,

statgen-setup login --tutorial pseq

R and PLINK

To run the exercise from docker image provided,

statgen-setup launch --tutorial plink-r-nothnagel

REGENIE

• REGENIE Exercise [PDF]
• REGENIE Exercise [Ipython Notebook]

To run the exercise from docker image provided,

statgen-setup launch --tutorial regenie

Then follow prompts on the terminal output to open up the JupyterLab server in your web browser. If it is the first time you start this server, please open a command terminal inside JupyterLab, and type

get-data

to load the data-set to the JupyterLab workspace.

Regression

• Regression Exercise [DOCX]
• Exercise Commands

To run the exercise from docker image provided,

statgen-setup login --tutorial regression

RV-TDT

• Exercise [DOC]
• Exercise Commands

Installing Packages

To install from packages, follow the configuration steps above and run the following command.

sudo apt-get install rvtdt-tutorial

The exercise's files will then be installed in the folder /home/shared/rvtdt. You can run from there or copy the files into your user's home directory and proceed with the exercise.

SEQLinkage

• SEQLinkage Exercise [PDF]
• Exercise Commands

To install from packages, follow the configuration steps above and run the following command.

sudo apt-get install seqlinkage-tutorial

The exercise's files will then be installed in the folder /home/shared/seqlinkage. You can run from there or copy the files into your user's home directory and proceed with the exercise.

SEQSpark

• SEQSpark Exercise [PDF]
• Exercise Commands
• Virtual Machine Image

Installing Packages

To install from packages, follow the configuration steps above and run the following command.

sudo apt-get install seqspark-tutorial

The exercise's files will then be installed in the folder /home/shared/seqspark. You can run from there or copy the files into your user's home directory and proceed with the exercise.In order for the commands to work correctly, you don't need to reboot, but you should log out and log back in to make sure that the computer's environment is correctly configured.

SLINK

• SLINK Exercise [DOCX]

To run the exercise from docker image provided,

statgen-setup login --tutorial slink

SUPERLINK

• SUPERLINK Exercise [PDF]
• Superlink

Variant Association Tools

• VAT Exercise [DOCX]
• VAT Exercise [Ipython notebook]

To run the exercise from docker image provided,

statgen-setup launch --tutorial vat

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.