Changes
From Statistical Genetics Courses
/* Variant Association Tools */
==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.
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==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==
* [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 in Exercise]]
To install from packages, follow the configuration steps above and run the following command.
<pre>sudo apt-get install annotation-tutorial</pre>
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.
==Annovar MEndelian==
* [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.research.bcm.edu/files/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://drive.google.com/file/d/0B2pJ9cgevF3sTS1DeGxYalFTN00/view Bam files for exercise]
==GenABEL==
* [http://statgen.us/files/tutorials/genabel/GenABEL_with_PLINK1.9.pdf GenABEL Exercise <nowiki>[PDF]</nowiki>]
* [[GeneABEL Exercise|Commands in ExerciseCommands]]
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==
* [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|Commands in ExerciseCommands]]
====Installing Packages====
==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|Commands in ExerciseCommands]]
====Installing Packages====
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== *[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/FastlinkageFastLinkage==
* [http://statgen.us/files/tutorials/SEQLinkage/linkage_intro_ex_berlin_2018_with_pg_num.pdf Linkage Introduction <nowiki>[PDF]</nowiki>]
==Population Genetics==
* [http://statgen.us/files/tutorials/population/Popgen_exe_ans.pdf Popgen Exercise <nowiki>[PDF]</nowiki>]
* [http://statgen.us/files/tutorials/population/popgen_drift.q Commands R Script for popgen_drift]* [http://statgen.us/files/tutorials/population/popgen_selection.q Commands R Script for popgen_selection]
==PSEQ==
* [http://statgen.us/files/tutorials/pseq/PSEQ_exercisePSEQ_exercise_2019.pdf PSEQ Exercise <nowiki>[PDF]</nowiki>]* [[PSEQ Commands in Exercise|Exercise Commands in Exercise]]
To install from packages, follow the configuration steps above and run the following command.
==Regression==
* [http://statgen.us/files/tutorials/regression_exercise.pdf Regression Exercise <nowiki>[PDF]</nowiki>]
* [[Regression_Exercise|Commands in ExerciseCommands]]
To install from packages, follow the configuration steps above and run the following command.
==RV-TDT==
* [http://statgen.us/files/tutorials/rvtdt/rvtdt_exerciservtdt_exercise_v3.pdf Exercise <nowiki>[PDF]</nowiki>]* [[RV-TDT|Commands in ExerciseCommands]]
====Installing Packages====
==SEQLinkage==
* [http://statgen.us/files/tutorials/SEQLinkage/SEQLinkage_revised_with_pg_numb.pdf SEQLinkage Exercise <nowiki>[PDF]</nowiki>]
* [[SEQLinkage_Commands_in_Exercise|Commands in ExerciseCommands]] 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==
* [http://statgen.us/files/tutorials/seqspark/SEQSpark_exercise_Final_v4.pdf SEQSpark Exercise <nowiki>[PDF]</nowiki>]
* [[SEQSpark|Commands in ExerciseCommands]]
* [http://statgen.us/files/images/SEQSpark.ova Virtual Machine Image]
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==
* [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==
* [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==
* [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 in Exercise]]
====Installing Packages====
<pre>sudo apt-get install vtools-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.
==VAT Mendelian==
* [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.
