Changes
From Statistical Genetics Courses
/* Running Tutorials on Your Computer */
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
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.
==AlohormaAlohomora==
* [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]
==Annotation==
* [http://statgen.us/files/tutorials/functional-annotation/FunctionalAnnotation_exercise_2018v2FunctionalAnnotation_exercise_2019.pdf Functional Annotation Exercise <nowiki>[PDF]</nowiki>]
* [[Commands in Annotation Exercise|Exercise Commands]]
==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==
* [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]]
==PSEQ==
* [http://statgen.us/files/tutorials/pseq/PSEQ_exercisePSEQ_exercise_2019.pdf PSEQ Exercise <nowiki>[PDF]</nowiki>]
* [[PSEQ Commands in Exercise|Exercise Commands]]
==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==
==SLINK==
* [http://statgen.us/files/tutorials/seqspark/slink_ex_short.pdf SLINK Exercise <nowiki>[PDF]</nowiki>]
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==
==Variant Association Tools==
* [http://statgen.us/files/tutorials/VAT_exercise_2018_nographsvat/VAT_exercise_2019_1_nographs.pdf VAT Exercise <nowiki>[PDF]</nowiki>]
* [[VAT Commands in Exercise|Exercise Commands]]
* [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.
