Changes
From Statistical Genetics Courses
/* IGV */
==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.
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.
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>echo "deb [trusted=yes] https://statgen.research.bcm.eduus/deb ./" | sudo tee -a /etc/apt/sources.list.d/statgen.list
sudo add-apt-repository -y ppa:webupd8team/java
sudo apt-get update
</pre>
==Alohomora==* [http://statgen.us/files/tutorials/seqspark/Alohomora_Exercise_revised.pdf Exercise <prenowiki> [PDF]</prenowiki>]* [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Data Set]* [http://gmc.mdc-berlin.de/alohomora/ Software Link]
==Annotation==
* [httphttps://statgengithub.uscom/filesstatgenetics/tutorials/functionalstatgen-annotationcourses/FunctionalAnnotation_exercise_2018v2blob/master/handout/FunctionalAnnotation.2019.pdf docx Functional Annotation Exercise <nowiki>[PDFDOCX]</nowiki>]
* [[Commands in Annotation Exercise|Exercise Commands]]
To install run the exercise from packagesdocker image provided, follow the configuration steps above <pre>statgen-setup login --tutorial annovar</pre> The "statgen-setup" script is available [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup here] and run the can be installed following command[https://github.com/statgenetics/statgen-courses/blob/master/README.md#prepare-your-computer-to-manage-the-tutorials these instructions].
==Annovar MEndelian==* [http://statgen.us/files/tutorials/FunctionalAnnotation_Annovar_final.pdf Exercise <prenowiki>sudo apt-get install annotation-tutorial[PDF]</prenowiki>]The exercise's * [https://statgen.research.bcm.edu/files will then be installed in the folder ''/home2017/shared09/commands/annovar-functional_annotation''. You can run from there or copy the txt Commands Part I - Functional Annotation]* [https://statgen.research.bcm.edu/files into your user's home directory and proceed with the exercise/2017/09/commands/annovar-variant_filtering.txt Commands Part II - Variant Filtering]
==Cochran Armitage Trend Test==
* [http://statgen.us/files/tutorials/Armitage_sample_size_Berlin_1Armitage_sample_size_revised.pdf CATT Exercise <nowiki>[PDF]</nowiki>]
==GATK and IGV==
====Result Files====
:* [http://statgen.us/files/2016/07/gatk_results.tar.gz GATK/IGV exercise]
==Gemini==
* [https://github.com/statgenetics/statgen-courses/blob/master/handout/Gemini.docx Gemini exercise <nowiki>[DOCX]</nowiki>]
To run the exercise from docker image provided,
<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].
==GenABEL==
<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==
* [http://statgen.us/files/tutorials/genehunter/Mult_Genehunter.pdf <nowiki>[PDF]</nowiki>]
* [[Genehunter Exercise|Exercise Commands]]
To install from packages, follow the configuration steps above and run the following command.
<pre>sudo apt-get install genehunter-tutorial</pre>
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==
* [http://statgen.us/files/tutorials/gwas-qc/PLINK_data_QCPLINK_data_QC_V2.pdf Exercise <nowiki>[PDF]</nowiki>]
* [[GWAS Data QC Exercise|Exercise Commands]]
==GWAS: Association Analysis Controlling for Population Substructure==
* [http://statgen.us/files/tutorials/gwas-substructure/GWAS_Data_Controlling_for_SubstructureGWAS_Data_Controlling_for_Substructure_V2.pdf Exercise <nowiki>[PDF]</nowiki>]
* [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]
<pre>sudo apt-get install plink-tutorial</pre>
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.
==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==
* [http://statgen.us/files/software/igv/igv-2.3.97.jar igv.jar Software Link]
* [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==
* [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/blob/master/SEQLinkagehandout/linkage_intro_ex_berlin_2018_with_pg_numMLINK.pdf Linkage Introduction LINKAGE Exercise <nowiki>[PDFDOCX]</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].
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==Population Genetics==
* [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/populationblob/Popgen_exe_ansmaster/handout/PopGen.pdf docx Popgen Exercise <nowiki>[PDFDOCX]</nowiki>]* To run the exercise from docker image provided, <pre>statgen-setup login --tutorial popgen</pre> The "statgen-setup" script is available [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/populationblob/popgen_drift.q Commands for popgen_driftmaster/src/statgen-setup here]* and can be installed following [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/populationblob/popgen_selectionmaster/README.q Commands for popgen_selectionmd#prepare-your-computer-to-manage-the-tutorials these instructions].
==PSEQ==
* [httphttps://statgengithub.uscom/filesstatgenetics/tutorialsstatgen-courses/pseqblob/PSEQ_exercisemaster/handout/PSEQ.pdf doc PSEQ Exercise <nowiki>[PDFDOCX]</nowiki>]
* [[PSEQ Commands in Exercise|Exercise Commands]]
To install run the exercise from packagesdocker image provided, follow the configuration steps above and run the following command.
<pre>sudo aptstatgen-setup login -get install plinkseq-tutorialpseq</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/pseq''statgenetics/statgen-courses/blob/master/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].
==Regression==
* [httphttps://statgengithub.uscom/statgenetics/statgen-courses/blob/filesmaster/tutorialshandout/regression_exerciseregression.pdf docx Regression Exercise <nowiki>[PDFDOCX]</nowiki>]
* [[Regression_Exercise|Exercise Commands]]
To install run the exercise from packagesdocker image provided, follow the configuration steps above and run the following command. <pre>statgen-setup login --tutorial regression</pre>
==RV-TDT==
* [http://statgen.us/files/tutorials/rvtdt/rvtdt_exerciservtdt_exercise_v3.pdf Exercise <nowiki>[PDF]</nowiki>]
* [[RV-TDT|Exercise Commands]]
* [http://statgen.us/files/tutorials/SEQLinkage/SEQLinkage_revised_with_pg_numb.pdf SEQLinkage Exercise <nowiki>[PDF]</nowiki>]
* [[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==
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==
* [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].
==SUPERLINK==
* [http://statgen.us/files/tutorials/Superlink_Exercise_v2.pdf SUPERLINK Exercise <nowiki>[PDF]</nowiki>]
* [https://statgen.research.bcm.edu/files/2016/10/data/superlink.zip Superlink]
==Variant Association Tools==
* [httphttps://statgenstatgenetics.usgithub.io/filesstatgen-courses/tutorialsnotebooks/VAT_exercise_2018_nographsVAT.pdf html VAT Exercise <nowiki>[PDFHTML]</nowiki>]
* [[VAT Commands in Exercise|Exercise Commands]]
To run the exercise from docker image provided, <pre>statgen-setup login --tutorial vat</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]. ==VAT Mendelian==Installing Packages====* [http://statgen.us/files/tutorials/VAT_Mendelian.pdf Exercise <nowiki>[PDF]</nowiki>]* [[VAT mendelian commands|Exercise Commands]]
To install from packages, follow the configuration steps above and run the following command.
<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.
