|
|
| (29 intermediate revisions by the same user not shown) |
| Line 1: |
Line 1: |
| | ==Tutorials for Courses== | | ==Tutorials for Courses== |
| − | * [[Tutorials#Annotation|ANNOVAR Annotation]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/annovar.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/annovar/tags docker image] | + | * [[Tutorials#FastLMM_&_GCTA|FastLMM & GCTA]] | [[Media:fastlmm_gcta_exercise.pdf|exercise [PDF]]] and [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta docker image] |
| − | * [[Tutorials#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
| + | * [[Tutorials#Mendelian Randomization|Mendelian Randomization]] | exercise [PDF] and docker image |
| − | * [[Tutorials#FastLMM | Family-based Association using FaST-LMM, PLINK and R]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/fastlmm-gcta.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta/tags docker image]
| + | * [[Tutorials#Pleiotropy|Pleiotropy]] | exercise [PDF] and docker image |
| − | * [[Tutorials#IGV|IGV]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/igv.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/igv/tags docker image] | + | * [[Tutorials#PLINK_GWAS:_Data_Quality_Control_and Association_Analysis_Controlling_for_Population_Substructure|PLINK GWAS: QC and Controlling for Population Substructure]] | [[Media:PLINK_Data_QC.pdf|QC exercise [PDF]]], [[Media:PLINK_Substructure.pdf|Substructure exercise [PDF]]], and [https://hub.docker.com/r/statisticalgenetics/plink-gwas docker image] |
| − | * [[Tutorials#Gemini|Gemini]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/gemini.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/gemini/tags docker image] | + | * [[Tutorials#REGENIE|REGENIE]] | [[Media:regenie.pdf|exercise [PDF]]] and [https://hub.docker.com/r/statisticalgenetics/regenie docker image] |
| − | * [[Tutorials#GCTA|GCTA]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/fastlmm-gcta.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta/tags docker image] | + | * [[Tutorials#Regression_and_Intro_to_PLINK_and_R|Regression and Intro to PLINK and R]] | [[Media:Regression.pdf|Regression exercise [PDF]]], [[Media:Intro_Plink_R.pdf|Intro to PLINK & R exercise[PDF]]], and [https://hub.docker.com/r/statisticalgenetics/regression-plink-r docker image] |
| − | * [[Tutorials#GWAS:_Data_Quality_Control|GWAS: QC]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/plink.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/plink/tags docker image]
| + | |
| − | * [[Tutorials#GWAS:_Association_Analysis_Controlling_for_Population_Substructure|GWAS: Controlling for Population Substructure]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/plink.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/plink/tags docker image]
| + | |
| − | * [[Tutorials#Epistasis_.28PLINK_and_CASSI.29 | Interaction analysis using PLINK and CASSI]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/epistasis.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/epistasis/tags docker image]
| + | |
| − | * [[Tutorials#Linkage.2FFastLinkage|LINKAGE]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/mlink.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/mlink/tags docker image]
| + | |
| − | * [[Tutorials#Population_Genetics|Population Genetics]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/popgen.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/popgen/tags docker image]
| + | |
| − | * [[Tutorials#Pleiotropy|Pleiotropy]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/pleiotropy.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/pleiotropy/tags docker image] | + | |
| − | * [[Tutorials#Polygenic_risk_prediction_.28NPS_method.29|Polygenic risk prediction using non-parametric shrinkage]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/nps.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/nps/tags docker image]
| + | |
| − | * [[Tutorials#PSEQ|PLINK/SEQ (PSEQ)]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/pseq.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/pseq/tags docker image] | + | |
| − | * [[Tutorials#R_and_PLINK|R and PLINK exercise]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/plink-r-nothnagel.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/plink-r-nothnagel/tags docker image]
| + | |
| − | * [[Tutorials#Regression|Regression]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/regression.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/regression/tags docker image]
| + | |
| − | * [[Tutorials#RV-TDT|RV-TDT]]
| + | |
| − | * [[Tutorials#SEQLinkage|SEQLinkage]]
| + | |
| − | * [[Tutorials#SEQSpark|SEQSpark]]
| + | |
| − | * [[Tutorials#SLINK|SLINK]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/slink.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/slink/tags docker image]
| + | |
| − | * [[Tutorials#Variant_Association_Tools|Variant Association Tools]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/vat.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/vat/tags docker image]
| + | |
| − | | + | |
| − | <!---
| + | |
| − | | + | |
| − | ==[[Genetic Meetings of Interest]]==
| + | |
| − | [[NGSMendelian2017|Identifying Genes for Mendelian Traits using Next Generation Sequence Data]], September 18-22, 2017<br />Max Delbrück Center for Molecular Medicine<br />Berlin, Germany
| + | |
| − | | + | |
| − | [[Genassoc2017|Genetic Association Course With Application to Sequence and Genotype Data]], June 26-30, 2017<br />Max Delbrück Center for Molecular Medicine<br />Berlin, Germany
| + | |
| − | | + | |
| − | [[ComplexNGS2017|Complex Trait Analysis of Next Generation Sequence Data]], March 6-10, 2017 <br />Max Delbrück Center for Molecular Medicine<br />Berlin, Germany
| + | |
| − | | + | |
| − | [[Advgenemap2017|Advanced Gene Mapping Course]], January 23-27, 2017 <br /> The Rockefeller University, New York
| + | |
| − | | + | |
| − | [[NGSMendelian2016|Identifying Genes for Mendelian Traits using Next Generation Sequence Data]], October 31-November 4, 2016<br />Max Delbrück Center for Molecular Medicine<br />Berlin, Germany
| + | |
| − | | + | |
| − | [[Genassoc2016|Genetic Association Course With Application to Sequence and Genotype Data]], September 5-9, 2016<br />Max Delbrück Center for Molecular Medicine<br />Berlin, Germany
| + | |
| − | | + | |
| − | [[ComplexNGS2016|Complex Trait Analysis of Next Generation Sequence Data]], July 4-8, 2016 <br />Max Delbrück Center for Molecular Medicine<br />Berlin, Germany
| + | |
| − | | + | |
| − | [[Advgenemap2016|Advanced Gene Mapping Course]], January 25-29, 2016 <br /> The Rockefeller University, New York
| + | |
| − | | + | |
| − | [https://www.bcm.edu/research/labs/center-for-statistical-genetics/courses/ngs-mendelian-course-sept-oct-2015 Identifying Genes for Mendelian Traits using Next Generation Sequence Data,] Sept. 28-Oct. 2, 2015<br />Max Delbrück Center (MDC) for Molecular Medicine<br />Berlin, Germany
| + | |
| − | | + | |
| − | [https://www.bcm.edu/research/labs/center-for-statistical-genetics/courses/genetic-association-course-june-2015 Genetic Association Course With Application to Sequence and Genotype Data], June 22-26, 2015<br />Max Delbrück Center for Molecular Medicine<br />Berlin, Germany
| + | |
| − | | + | |
| − | [[2015MarchMDC|Complex Trait Analysis of Next Generation Sequence Data]], March 23-27, 2015<br />Max Delbrück Center for Molecular Medicine<br />Berlin, Germany
| + | |
| − | | + | |
| − | [[2015AdvancedGeneMapping|Advanced Gene Mapping Course]], Feb. 9-13, 2015 <br />The Rockefeller University, New York
| + | |
| − | | + | |
| − | [https://www.bcm.edu/research/labs/center-for-statistical-genetics/courses/next-generation-sequence-data-course-jun-2014 Analysis of Next Generation Sequence Data Course,]June 23-27, 2014<br />Max Delbrück Center for Molecular Medicine<br />Berlin, Germany
| + | |
| − | | + | |
| − | [https://www.bcm.edu/research/labs/center-for-statistical-genetics/courses/genetic-association-course-march-2014 Genetic Association Course], March 3-7, 2014<br />Max Delbrück Center for Molecular Medicine<br />Berlin, Germany
| + | |
| − | | + | |
| − | [https://www.bcm.edu/research/labs/center-for-statistical-genetics/courses/advanced-gene-mapping-course-jan-2014 Advanced Gene Mapping Course], Jan. 27-31, 2014<br />The Rockefeller University<br />New York, NY
| + | |
| − | | + | |
| − | [https://www.bcm.edu/research/labs/center-for-statistical-genetics/courses/genetic-association-course-june-2013 Genetic Association Course], June 3-7, 2013<br />With Application to Analysis of Sequence and Genotype Data<br />Max Delbrück Center for Molecular Medicine<br />Berlin, Germany
| + | |
| − | | + | |
| − | [https://www.bcm.edu/research/labs/center-for-statistical-genetics/courses/advanced-gene-mapping-course-jan-2013 Advanced Gene Mapping Course], Jan. 28 -Feb. 1, 2013<br />The Rockefeller University<br />New York, NY
| + | |
| − | | + | |
| − | [http://linkage.rockefeller.edu/suzanne/Berlin_Basic_Gene_Mapping_Course_2012.htm Basic Gene Mapping Course], Nov. 26-30, 2012<br />Max Delbrück Center for Molecular Medicine<br />Berlin, Germany
| + | |
| − | | + | |
| − | [http://linkage.rockefeller.edu/suzanne/Berlin_Genetic_Association_Course_2012.html Genetic Association Course], July 23-27, 2012<br />Max Delbrück Center for Molecular Medicine<br />Berlin, Germany
| + | |
| − | | + | |
| − | [http://linkage.rockefeller.edu/suzanne/advanced_course_Jan_12 Advanced Gene Mapping Course], Jan. 16-20, 2012<br />The Rockefeller University<br />New York, NY
| + | |
| − | | + | |
| − | [http://linkage.rockefeller.edu/suzanne/Berlin_Basic_Gene_Mapping_Course_2011.htm Basic Gene Mapping Course], Nov. 7-11, 2011<br />Max Delbrück Center (MDC) for Molecular Medicine<br />Berlin, Germany
| + | |
| − | | + | |
| − | [http://linkage.rockefeller.edu/suzanne/Berlin_Genetic_Association_Course_2011.html Genetic Association Course], July 4-8, 2011<br />Max Delbrück Center (MDC) for Molecular Medicine<br />Berlin, Germany
| + | |
| − | | + | |
| − | [http://linkage.rockefeller.edu/suzanne/BCM_Association_Course_2011.html Genetic Association Course], March 22-25, 2011<br />Center for Statistical Genetics<br />Baylor College of Medicine<br />Houston, TX
| + | |
| − | | + | |
| − | [https://www.bcm.edu/research/labs/center-for-statistical-genetics/courses/advanced-gene-mapping-course-dec-2010 Advanced Gene Mapping Course], Dec. 13-17, 2010<br />The Rockefeller University <br />New York, NY
| + | |
| − | | + | |
| − | [http://linkage.rockefeller.edu/suzanne/MDC_Berlin_Basic_Gene_Mapping_Course_2010.htm Basic Gene Mapping Course], Oct. 25-29, 2010<br />Max Delbrück Center (MDC) for Molecular Medicine<br />Berlin, Germany
| + | |
| − | | + | |
| − | [http://linkage.rockefeller.edu/suzanne/MDC_Berlin_Association_Course_2010.html Genetic Association Course], May 3-7, 2010<br />Max Delbrück Center (MDC) for Molecular Medicine<br />Berlin, Germany
| + | |
| − | -->
| + | |
| − | ==Genetic Analysis Software==
| + | |
| − | More information about the software used in the previous courses can be found here https://gaow.github.io/genetic-analysis-software/0/
| + | |
| | | | |
| | ==Running Tutorials on Your Computer== | | ==Running Tutorials 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) or even a high performance computing cluster (if properly configured) for your own data analysis.
| + | We adopt [https://www.docker.com/ docker] to run our course material, and we have created various [https://hub.docker.com/u/statisticalgenetics docker repositories] with freely available Docker images for users to readily run our exercises on their own computers using [https://docs.docker.com/desktop/ Docker Desktop]. These docker images are for multi-platform use (Mac, Windows, or Linux). More information regarding instructions to install Docker Desktop and to run the course material on your computer is detailed in the documentation below. |
| | | | |
| | ===General instructions=== | | ===General instructions=== |
| − | * [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#alternative-to-cloud-server-use-your-own-computer Instructions to setup course tutorial environment on your computer] | + | * [[Media:Statistical_Genetics_Exercise_Instructions.pdf|Instructions to install Docker Desktop and running the course material on your computer]] |
| − | * [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#option-1-launch-exercise-in-jupyterlab Instructions to run course tutorial through JupyterLab]
| + | |
| − | * [https://github.com/statgenetics/statgen-courses/wiki/How-to-launch-course-tutorials#option-2-launch-from-command-shell Instructions to run course tutorial through command line terminal]
| + | |
| − | | + | |
| − | ===Preparing Your Computer===
| + | |
| − | {| class="wikitable"
| + | |
| − | |-
| + | |
| − | ||{{#ev:youtube|3K-sGzxsyK0|240|center|Linux}}
| + | |
| − | ||{{#ev:youtube|DRCDNBlxZ-w|240|center|Mac}}
| + | |
| − | ||{{#ev:youtube|sxv45NCSFMk|240|center|Windows}}
| + | |
| − | |}
| + | |
| − | | + | |
| − | ===Running Exercises===
| + | |
| − | {{#ev:youtube|OgHvRVtIIog|320}}
| + | |
| | | | |
| | ===Tutorial specific instructions=== | | ===Tutorial specific instructions=== |
| − | We use a script [https://github.com/statgenetics/statgen-courses/blob/master/src/statgen-setup "statgen-setup"] to start the docker based environments for these tutorials. Please refer to the previous section for instructions on the installation of this script.
| + | Please refer to the previous section for instructions on the installation of Docker Desktop and basic usages. |
| | | | |
| − | 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. Command "statgen-setup login" will allow you to start and login to a Linux command line environment (regardless of your current computational environment) to perform all analysis in command shells. This works for all the tutorials on this page. Additionally, some tutorials support command "statgen-setup launch" which will start a JupyterLab server to perform the analysis. | + | Material and instructions for specific exercise are listed in each section below. They provide links to pdf versions of the exercises and a minimal set of commands to use for downloading the docker images and running an exercise. |
| | | | |
| − | ==Alohomora== | + | ==FastLMM & GCTA== |
| − | * [http://statgen.us/files/tutorials/Alohomora_Exercise_revised.pdf Exercise <nowiki>[PDF]</nowiki>] | + | * [[Media:fastlmm_gcta_exercise.pdf|FastLMM & GCTA exercise]] [https://github.com/statgenetics/statgen-courses/blob/master/handout/GCTA.pdf <nowiki>[PDF]</nowiki>] |
| − | * [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Data Set] | + | * [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta FastLMM & GCTA docker image] |
| − | * [http://gmc.mdc-berlin.de/alohomora/ Software Link]
| + | |
| | | | |
| − | ==Annovar complex traits==
| + | To pull and download the docker image from the Docker Hub repository, |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/FunctionalAnnotation.pdf Functional Annotation Exercise <nowiki>[PDF]</nowiki>]
| + | |
| − | * [[Commands in Annotation Exercise|Exercise Commands]]
| + | |
| | | | |
| − | To run the exercise from docker image provided, | + | <pre>docker pull statisticalgenetics/fastlmm-gcta</pre> |
| | + | To run the exercise from the downloaded docker image, |
| | | | |
| − | <pre>statgen-setup login --tutorial annovar | + | <pre>docker run --rm -p 8888:8888 statisticalgenetics/fastlmm-gcta</pre> |
| − | </pre> | + | |
| | | | |
| − | ==Annovar Mendelian traits== | + | ==Mendelian Randomization== |
| − | * [http://statgen.us/files/tutorials/FunctionalAnnotation_Annovar_final.pdf Exercise <nowiki>[PDF]</nowiki>] | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/GCTA.pdf Mendelian Randomization exercise <nowiki>[PDF]</nowiki>] |
| − | * [https://statgen.us/files/2017/09/commands/annovar-functional_annotation.txt Commands Part I - Functional Annotation] | + | * Mendelian Randomization docker image |
| − | * [https://statgen.us/files/2017/09/commands/annovar-variant_filtering.txt Commands Part II - Variant Filtering]
| + | |
| | | | |
| − | ==Cochran Armitage Trend Test==
| + | To pull and download the docker image from the Docker Hub repository, |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/Armitage_sample_size.pdf CATT Exercise <nowiki>[PDF]</nowiki>]
| + | |
| | | | |
| | + | <pre>docker pull statisticalgenetics/mendelian-randomization</pre> |
| | + | To run the exercise from the downloaded docker image, |
| | | | |
| − | | + | <pre>docker run --rm -p 8888:8888 statisticalgenetics/mendelian-randomization</pre> |
| − | ==Epistasis (PLINK and CASSI)==
| + | |
| − | * [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>
| + | |
| − | | + | |
| − | | + | |
| − | ==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>
| + | |
| − | | + | |
| − | | + | |
| − | ==Fine-mapping (SuSiE method)==
| + | |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/finemapping.docx susieR Exercise <nowiki>[DOCX]</nowiki>]
| + | |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/finemapping_answers.docx susieR Exercise Answers <nowiki>[DOCX]</nowiki>]
| + | |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/finemapping.ipynb susieR Exercise <nowiki>[Ipython notebook]</nowiki>]
| + | |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/finemapping_answers.ipynb susieR Exercise Answers <nowiki>[Ipython notebook]</nowiki>]
| + | |
| − | | + | |
| − | | + | |
| − | To run the exercise from docker image provided,
| + | |
| − | | + | |
| − | <pre>statgen-setup launch --tutorial finemap
| + | |
| − | </pre>
| + | |
| − | | + | |
| − | ==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>
| + | |
| − | | + | |
| − | | + | |
| − | ==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>
| + | |
| − | | + | |
| − | | + | |
| − | ==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==
| + | |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_data_QC.pdf Exercise <nowiki>[PDF]</nowiki>]
| + | |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PLINK_Data_QC.ipynb Exercise <nowiki>[IPython Notebook]</nowiki>]
| + | |
| − | * [[GWAS Data QC Exercise|Exercise Commands]]
| + | |
| − | | + | |
| − | To run the exercise via JupyterLab from docker image provided,
| + | |
| − | | + | |
| − | <pre>statgen-setup launch --tutorial plink
| + | |
| − | </pre>
| + | |
| − | | + | |
| − | Alternatively, you can opt to run the exercise via command terminal from docker image provided,
| + | |
| − | | + | |
| − | <pre>statgen-setup login --tutorial plink
| + | |
| − | </pre>
| + | |
| − | | + | |
| − | ==GWAS: Association Analysis Controlling for Population Substructure==
| + | |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/PLINK_Substructure.pdf Exercise <nowiki>[PDF]</nowiki>]
| + | |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PLINK_Substructure.ipynb Exercise <nowiki>[IPython Notebook]</nowiki>]
| + | |
| − | * [[GWAS_Controlling_for_Population_Substructure|Exercise Commands]]
| + | |
| − | | + | |
| − | To run the exercise via JupyterLab from docker image provided,
| + | |
| − | | + | |
| − | <pre>statgen-setup launch --tutorial plink
| + | |
| − | </pre>
| + | |
| − | | + | |
| − | Alternatively, you can opt to run the exercise via command terminal from docker image provided,
| + | |
| − | | + | |
| − | <pre>statgen-setup login --tutorial plink
| + | |
| − | </pre>
| + | |
| − | | + | |
| − | ==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)]
| + | |
| − | | + | |
| − | | + | |
| − | | + | |
| − | ==Linkage/FastLinkage==
| + | |
| − | * [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>
| + | |
| − | | + | |
| − | ==LD clumping==
| + | |
| − | * [https://github.com/cumc/bioworkflows/blob/master/GWAS/LD_Clumping.ipynb LD Clumping Exercise <nowiki>[IPython Notebook]</nowiki>]
| + | |
| − | | + | |
| − | | + | |
| − | To run the exercise from docker image provided,
| + | |
| − | | + | |
| − | <pre>statgen-setup launch --tutorial clumping
| + | |
| − | </pre>
| + | |
| − | | + | |
| − | ==MR-JTI for TWAS==
| + | |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/MR_JTI.ipynb MR-JTI Exercise <nowiki>[IPython Notebook]</nowiki>]
| + | |
| − | | + | |
| − | | + | |
| − | To run the exercise from docker image provided,
| + | |
| − | | + | |
| − | <pre>statgen-setup launch --tutorial twas
| + | |
| − | </pre> | + | |
| | | | |
| | ==Pleiotropy== | | ==Pleiotropy== |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy.pdf Pleiotropy Exercise <nowiki>[PDF]</nowiki>] | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy.pdf Pleiotropy Exercise <nowiki>[PDF]</nowiki>] |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy_answers.pdf Pleiotropy Answers to Questions <nowiki>[PDF]</nowiki>] | + | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/Pleiotropy_answers.pdf Pleiotropy docker image] |
| | | | |
| − | To run the exercise from docker image provided,
| + | To pull and download the docker image from the Docker Hub repository, |
| | | | |
| − | <pre>statgen-setup login --tutorial pleiotropy | + | <pre>docker pull statisticalgenetics/pleiotropy</pre> |
| − | </pre> | + | To run the exercise from the downloaded docker image, |
| | | | |
| | + | <pre>docker run --rm -p 8888:8888 statisticalgenetics/pleiotropy</pre> |
| | | | |
| − | ==Polygenic risk prediction (NPS method)== | + | ==PLINK GWAS: Data Quality Control and Association Analysis Controlling for Population Substructure== |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/NPS.pdf PRS NPS Exercise <nowiki>[DOCX]</nowiki>]
| + | These exercises run using a shared docker image, however the exercises are split into two separate notebooks. |
| | | | |
| − | To run the exercise from docker image provided,
| + | * [[Media:PLINK_Data_QC.pdf|PLINK GWAS: Data QC Exercise <nowiki>[PDF]</nowiki>]] |
| | + | * [[Media:PLINK_Substructure.pdf|PLINK GWAS: Population Substructure Exercise <nowiki>[PDF]</nowiki>]] |
| | + | * [https://hub.docker.com/r/statisticalgenetics/plink-gwas PLINK GWAS docker image] |
| | | | |
| − | <pre>statgen-setup login --tutorial nps
| + | To pull and download the docker image from the Docker Hub repository, |
| − | </pre>
| + | |
| | | | |
| | + | <pre>docker pull statisticalgenetics/plink-gwas</pre> |
| | + | To run the exercise from the downloaded docker image, |
| | | | |
| − | ==Polygenic risk prediction (LDpred2 method)==
| + | <pre>docker run --rm -p 8888:8888 statisticalgenetics/plink-gwas</pre> |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/ldpred2_example.pdf PRS LDpred2 Exercise <nowiki>[PDF]</nowiki>]
| + | |
| − | * [https://github.com/cumc/bioworkflows/blob/master/ldpred/ldpred2_example.ipynb PRS LDpred2 Exercise <nowiki>[Ipython Notebook]</nowiki>]
| + | |
| − | | + | |
| − | | + | |
| − | To run the exercise from docker image provided,
| + | |
| − | | + | |
| − | <pre>statgen-setup launch --tutorial ldpred2
| + | |
| − | </pre>
| + | |
| − | | + | |
| − | Then follow prompts on the terminal output to open up the JupyterLab server in your web browser. If it is the first time you start this server, please open a command terminal inside JupyterLab, and type
| + | |
| − | | + | |
| − | <pre>get-data</pre>
| + | |
| − | | + | |
| − | to load the data-set to the JupyterLab workspace.
| + | |
| − | | + | |
| − | | + | |
| − | <!--
| + | |
| − | ==Population Genetics==
| + | |
| − | * [http://statgen.us/files/tutorials/population/berlinseq.2.2.PopGen_exercise.pdf Population Exercise <nowiki>[PDF]</nowiki>]
| + | |
| − | * [http://statgen.us/files/tutorials/population/berlinseq.2.2.PopGen_answers.pdf Exercise Answers <nowiki>[PDF]</nowiki>]
| + | |
| − | * [http://statgen.us/files/tutorials/population/popgen_drift.q Commands for popgen_drift]
| + | |
| − | * [http://statgen.us/files/tutorials/population/popgen_selection.q Commands for popgen_selection]
| + | |
| − | -->
| + | |
| − | ==Population Genetics==
| + | |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/PopGen.docx Popgen Exercise <nowiki>[DOCX]</nowiki>]
| + | |
| − | | + | |
| − | | + | |
| − | To run the exercise from docker image provided,
| + | |
| − | | + | |
| − | <pre>statgen-setup login --tutorial popgen
| + | |
| − | </pre>
| + | |
| − | | + | |
| − | | + | |
| − | ==PSEQ==
| + | |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/PSEQ.pdf PSEQ Exercise <nowiki>[PDF]</nowiki>]
| + | |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/PSEQ.ipynb PSEQ Exercise <nowiki>[Ipython Notebook]</nowiki>]
| + | |
| − | | + | |
| − | To run the exercise from docker image provided,
| + | |
| − | | + | |
| − | <pre>statgen-setup launch --tutorial pseq
| + | |
| − | </pre>
| + | |
| − | | + | |
| − | Notice that since PSEQ exercise does not involve generating and visualizing plots, it is also fine to use a command terminal, instead of the JupyterLab server, to run this exercise and reproduce exactly what was described in the tutorial. To do so,
| + | |
| − | | + | |
| − | <pre>statgen-setup login --tutorial pseq
| + | |
| − | </pre>
| + | |
| − | | + | |
| − | | + | |
| − | ==R and PLINK==
| + | |
| − | To run the exercise from docker image provided,
| + | |
| − | | + | |
| − | <pre>statgen-setup launch --tutorial plink-r-nothnagel
| + | |
| − | </pre> | + | |
| − | | + | |
| | | | |
| | ==REGENIE== | | ==REGENIE== |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/regenie_example.pdf REGENIE Exercise <nowiki>[PDF]</nowiki>] | + | * [[Media:regenie.pdf|Regenie Exercise <nowiki>[PDF]</nowiki>]] |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/regenie_example.ipynb REGENIE Exercise <nowiki>[Ipython Notebook]</nowiki>]
| + | * [https://hub.docker.com/r/statisticalgenetics/regenie Regenie docker image] |
| − | | + | |
| − | | + | |
| − | To run the exercise from docker image provided,
| + | |
| − | | + | |
| − | <pre>statgen-setup launch --tutorial regenie
| + | |
| − | </pre>
| + | |
| − | | + | |
| − | Then follow prompts on the terminal output to open up the JupyterLab server in your web browser. If it is the first time you start this server, please open a command terminal inside JupyterLab, and type
| + | |
| − | | + | |
| − | <pre>get-data</pre>
| + | |
| − | | + | |
| − | to load the data-set to the JupyterLab workspace.
| + | |
| − | | + | |
| − | | + | |
| − | | + | |
| − | ==Regression==
| + | |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/regression.docx Regression Exercise <nowiki>[DOCX]</nowiki>]
| + | |
| − | * [[Regression_Exercise|Exercise Commands]]
| + | |
| − | | + | |
| − | To run the exercise from docker image provided,
| + | |
| − | | + | |
| − | <pre>statgen-setup login --tutorial regression
| + | |
| − | </pre>
| + | |
| − | | + | |
| − | | + | |
| − | ==RV-TDT==
| + | |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/RV-TDT.doc Exercise <nowiki>[DOC]</nowiki>]
| + | |
| − | * [[RV-TDT|Exercise Commands]]
| + | |
| − | | + | |
| − | ====Installing Packages====
| + | |
| − | To install from packages, follow the configuration steps above and run the following command.
| + | |
| − | | + | |
| − | <pre>sudo apt-get install rvtdt-tutorial</pre>
| + | |
| − | 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==
| + | |
| − | * [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==
| + | |
| − | * [http://statgen.us/files/tutorials/seqspark/SEQSpark_exercise_Final_v4.pdf SEQSpark Exercise <nowiki>[PDF]</nowiki>]
| + | |
| − | * [[SEQSpark|Exercise Commands]]
| + | |
| − | * [http://statgen.us/files/images/SEQSpark.ova Virtual Machine Image] | + | |
| − | | + | |
| − | ====Installing Packages====
| + | |
| − | To install from packages, follow the configuration steps above and run the following command.
| + | |
| − | | + | |
| − | <pre>sudo apt-get install seqspark-tutorial</pre>
| + | |
| − | 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,
| + | To pull and download the docker image from the Docker Hub repository, |
| | | | |
| − | <pre>statgen-setup login --tutorial slink</pre> | + | <pre>docker pull statisticalgenetics/regenie</pre> |
| | + | To run the exercise from the downloaded docker image, |
| | | | |
| − | ==SUPERLINK==
| + | <pre>docker run --rm -p 8888:8888 statisticalgenetics/regenie</pre> |
| − | * [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== | + | ==Regression and Intro to PLINK and R== |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/handout/VAT.docx VAT Exercise <nowiki>[DOCX]</nowiki>]
| + | These exercises run using a shared docker image, however the exercises are split into two separate notebooks. |
| − | * [https://github.com/statgenetics/statgen-courses/blob/master/notebooks/VAT.ipynb VAT Exercise <nowiki>[Ipython notebook]</nowiki>]
| + | |
| | | | |
| | + | * [[Media:Regression.pdf|Regression exercise [PDF]]] |
| | + | * [[Media:Intro_Plink_R.pdf|Intro to PLINK & R Exercise <nowiki>[PDF]</nowiki>]] |
| | + | * [https://hub.docker.com/r/statisticalgenetics/regression-plink-r Regression and Intro to PLINK & R docker image] |
| | | | |
| − | To run the exercise from docker image provided,
| + | To pull and download the docker image from the Docker Hub repository, |
| | | | |
| − | <pre>statgen-setup launch --tutorial vat | + | <pre>docker pull statisticalgenetics/regression-plink-r</pre> |
| − | </pre> | + | To run the exercise from the downloaded docker image, |
| | | | |
| − | Then follow the prompts on the terminal output to open up the JupyterLab server in your web browser. You should find the exercise notebook in the side panel, and you can click to open it.
| + | <pre>docker run --rm -p 8888:8888 statisticalgenetics/regression-plink-r</pre> |
Please refer to the previous section for instructions on the installation of Docker Desktop and basic usages.
Material and instructions for specific exercise are listed in each section below. They provide links to pdf versions of the exercises and a minimal set of commands to use for downloading the docker images and running an exercise.
These exercises run using a shared docker image, however the exercises are split into two separate notebooks.
These exercises run using a shared docker image, however the exercises are split into two separate notebooks.
