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) 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.
+
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.
  
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.
+
===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>.
  
<pre>echo "deb [trusted=yes] https://statgen.us/deb ./" | sudo tee -a /etc/apt/sources.list.d/statgen.list
+
====Mac and Linux users====
sudo add-apt-repository -y ppa:webupd8team/java
+
<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.
sudo apt-get update
+
 
</pre>
+
Finally please download our utility script [https://raw.githubusercontent.com/statgenetics/statgen-courses/master/src/statgen-setup <code>src/statgen-setup</code>] to your <code>PATH</code> and change it to executable, eg, <code>chmod +x ~/bin/statgen-setup</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.
  
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===
 +
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. For advanced options and other features provided by our utility script please read here our [https://github.com/statgenetics/statgen-courses/blob/master/README.md complete documentation to the utility script].
  
 
==Alohomora==
 
==Alohomora==
Line 19: Line 27:
  
 
==Annotation==
 
==Annotation==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.2019.docx Functional Annotation Exercise <nowiki>[DOCX]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.docx Functional Annotation Exercise <nowiki>[DOCX]</nowiki>]
 
* [[Commands in Annotation Exercise|Exercise Commands]]
 
* [[Commands in Annotation Exercise|Exercise Commands]]
  
 
To run the exercise from docker image provided,
 
To run the exercise from docker image provided,
  
<pre>
+
<pre>statgen-setup login --tutorial annovar
docker pull statisticalgenetics/annovar
+
statgen-setup login --tutorial annovar
+
 
</pre>
 
</pre>
  
Line 37: Line 43:
  
 
==Cochran Armitage Trend Test==
 
==Cochran Armitage Trend Test==
* [http://statgen.us/files/tutorials/Armitage_sample_size_revised.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>
 +
 
 +
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==
 +
* [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>
 +
 
 +
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].
 +
 
 +
==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==
 
==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]]
+
<pre>statgen-setup login --tutorial gemini
 +
</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 install from packages, follow the configuration steps above and run the following command.
 
  
<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==
Line 72: Line 102:
  
 
==GWAS: Data Quality Control==
 
==GWAS: Data Quality Control==
* [http://statgen.us/files/tutorials/gwas-qc/PLINK_data_QC_V2.pdf Exercise <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_data_QC.docx Exercise <nowiki>[PDF]</nowiki>]
 
* [[GWAS Data QC Exercise|Exercise Commands]]
 
* [[GWAS Data QC Exercise|Exercise Commands]]
  
====Installing Packages====
+
To run the exercise from docker image provided,
To install from packages, follow the configuration steps above and run the following command.
+
 
 +
<pre>statgen-setup login --tutorial plink
 +
</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].
 +
 
  
<pre>sudo apt-get install plink-tutorial</pre>
 
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.
 
  
 
==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_V2.pdf Exercise <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_Substructure.docx Exercise <nowiki>[PDF]</nowiki>]
 
* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]
 
* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]
  
====Installing Packages====
+
To run the exercise 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 login --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>
  
==Homozygosity Mapper==
+
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].
*[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]
+
==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>statgen-setup login --tutorial igv
 +
</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].
  
 
==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>
 +
 
 +
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].
 +
 
 +
==Pleiotropy==
 +
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy.docx Pleiotropy Exercise <nowiki>[DOCX]</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].
  
 
<!--
 
<!--
Line 111: Line 183:
 
-->
 
-->
 
==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>
 +
 
 +
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].
  
 
==PSEQ==
 
==PSEQ==
* [http://statgen.us/files/tutorials/pseq/PSEQ_exercise_2019.pdf PSEQ Exercise <nowiki>[PDF]</nowiki>]
+
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/PSEQ.doc PSEQ Exercise <nowiki>[DOCX]</nowiki>]
 
* [[PSEQ Commands in Exercise|Exercise Commands]]
 
* [[PSEQ Commands in 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 plinkseq-tutorial</pre>
+
<pre>statgen-setup login --tutorial pseq
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.
+
</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].
  
 
==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>sudo apt-get install regression-tutorial</pre>
+
<pre>statgen-setup login --tutorial regression
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.
+
</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].
  
 
==RV-TDT==
 
==RV-TDT==
* [http://statgen.us/files/tutorials/rvtdt/rvtdt_exercise_v3.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 166: Line 248:
  
 
==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>
 +
 +
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 install from packages, follow the configuration steps above and run the following command.
 
  
<pre>sudo apt-get install slink-tutorial</pre>
 
The exercise's files will then be installed in the folder ''/home/shared/slink''. You can run from there or copy the files into your user's home directory and proceed with the exercise.
 
  
 
==SUPERLINK==
 
==SUPERLINK==
Line 179: Line 264:
  
 
==Variant Association Tools==
 
==Variant Association Tools==
* [http://statgen.us/files/tutorials/vat/VAT_exercise_2019_1_nographs.pdf VAT Exercise <nowiki>[PDF]</nowiki>]
+
* [https://statgenetics.github.io/statgen-courses/notebooks/VAT.html VAT Exercise <nowiki>[HTML]</nowiki>]
 
* [[VAT Commands in Exercise|Exercise Commands]]
 
* [[VAT Commands in Exercise|Exercise Commands]]
  
====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.
+
 
+
==VAT Mendelian==
+
* [http://statgen.us/files/tutorials/VAT_Mendelian.pdf Exercise <nowiki>[PDF]</nowiki>]
+
* [[VAT mendelian commands|Exercise Commands]]
+
  
 +
<pre>statgen-setup login --tutorial vat
 +
</pre>
  
To install from packages, follow the configuration steps above and run the following command.
+
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].
 
+
<pre>sudo apt-get install vtools-mendelian-tutorial</pre>
+
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.
+

Revision as of 04:23, 25 February 2020

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) for your own data analysis.

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 SoS (a workflow system to run our course utility script) and docker.

Mac and Linux users

SoS requires Python 3.6+ to run. It is recommended that you install Miniconda to run Python 3 if you don't have it already. Once you have Python 3 installed, simply type pip install sos to install SoS, or, check out here for alternative installation methods if you have troubles with that command. To install docker from command line please follow our instructions here. Alternatively Mac users can download docker app for Mac and install from a graphical interface.

Finally please download our utility script src/statgen-setup to your PATH and change it to executable, eg, chmod +x ~/bin/statgen-setup if you put it under ~/bin which is part of your PATH. To verify your setup, type:

statgen-setup -h

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

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. For advanced options and other features provided by our utility script please read here our complete documentation to the utility script.

Alohomora

Annotation

To run the exercise from docker image provided,

statgen-setup login --tutorial annovar

The "statgen-setup" script is available here and can be installed following these instructions.

Annovar MEndelian

Cochran Armitage Trend Test


Epistasis (PLINK and CASSI)

To run the exercise from docker image provided,

statgen-setup login --tutorial epistasis

The "statgen-setup" script is available here and can be installed following these instructions.


FastLMM

To run the exercise from docker image provided,

statgen-setup login --tutorial fastlmm-gcta

The "statgen-setup" script is available here and can be installed following these instructions.

GCTA

To run the exercise from docker image provided,

statgen-setup login --tutorial fastlmm-gcta

The "statgen-setup" script is available here and can be installed following these instructions.

Gemini

To run the exercise from docker image provided,

statgen-setup login --tutorial gemini

The "statgen-setup" script is available here and can be installed following these instructions.


Genehunter


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

To run the exercise from docker image provided,

statgen-setup login --tutorial plink

The "statgen-setup" script is available here and can be installed following these instructions.


GWAS: Association Analysis Controlling for Population Substructure

To run the exercise from docker image provided,

statgen-setup login --tutorial plink

The "statgen-setup" script is available here and can be installed following these instructions.


Homozygosity Mapper

IGV

To run the exercise from docker image provided,

statgen-setup login --tutorial igv

The "statgen-setup" script is available here and can be installed following these instructions.

Linkage/FastLinkage


To run the exercise from docker image provided,

statgen-setup login --tutorial mlink

The "statgen-setup" script is available here and can be installed following these instructions.

Pleiotropy

To run the exercise from docker image provided,

statgen-setup login --tutorial pleiotropy

The "statgen-setup" script is available here and can be installed following these instructions.

Polygenic risk prediction (NPS method)

To run the exercise from docker image provided,

statgen-setup login --tutorial nps

The "statgen-setup" script is available here and can be installed following these instructions.

Population Genetics


To run the exercise from docker image provided,

statgen-setup login --tutorial popgen

The "statgen-setup" script is available here and can be installed following these instructions.

PSEQ

To run the exercise from docker image provided,

statgen-setup login --tutorial pseq

The "statgen-setup" script is available here and can be installed following these instructions.

Regression

To run the exercise from docker image provided,

statgen-setup login --tutorial regression

The "statgen-setup" script is available here and can be installed following these instructions.

RV-TDT

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


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

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

To run the exercise from docker image provided,

statgen-setup login --tutorial slink

The "statgen-setup" script is available here and can be installed following these instructions.


SUPERLINK

Variant Association Tools


To run the exercise from docker image provided,

statgen-setup login --tutorial vat

The "statgen-setup" script is available here and can be installed following these instructions.