Changes
From Statistical Genetics Courses
/* Variant Association Tools */
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.
