Statistical Genetics Courses - User contributions [en]

Main Page

2026-02-12T00:03:20Z

Serveradmin: /* Statistical Genetics Courses */

__NOTOC__

==Statistical Genetics Training Resources==
We are an international group of statistical geneticists who wish to make training resources available to the genetics community. We offer tutorials for a variety of analysis tools/software. We also offer courses on a variety of topics related to analysis of human genetic data.

===Our group===
* Heather Cordell, Ph.D. (Newcastle University)
* Andrew DeWan, Ph.D. (Yale University)
* Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University)
* Michael Nothnagel, Ph.D. (University of Cologne)
* Gao T. Wang, Ph.D. (Columbia University)

Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses

For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions

==Statistical Genetics Courses==
'''[[Advgenemap2026|Advanced Gene Mapping]]''' (January 11-15 2027) tenative The Rockefeller University, New York, USA

'''[[GABeyond2026|Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology]]''' September 14-18, 2026 The Max Delbrück Center, Berlin, Germany

 
[[Previous_Courses|Previous Course Pages]]

==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#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[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#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#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#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#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]

Main Page

2026-02-02T11:18:29Z

Serveradmin: /* Statistical Genetics Courses */

__NOTOC__

==Statistical Genetics Training Resources==
We are an international group of statistical geneticists who wish to make training resources available to the genetics community. We offer tutorials for a variety of analysis tools/software. We also offer courses on a variety of topics related to analysis of human genetic data.

===Our group===
* Heather Cordell, Ph.D. (Newcastle University)
* Andrew DeWan, Ph.D. (Yale University)
* Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University)
* Michael Nothnagel, Ph.D. (University of Cologne)
* Gao T. Wang, Ph.D. (Columbia University)

Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses

For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions

==Statistical Genetics Courses==
'''[[Advgenemap2026|Advanced Gene Mapping]]''' Late 2026 or Early 2027 The Rockefeller University, New York, USA

'''[[GABeyond2026|Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology]]''' September 14-18, 2026 The Max Delbrück Center, Berlin, Germany

 
[[Previous_Courses|Previous Course Pages]]

==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#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[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#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#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#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#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]

GABeyond2026

2026-01-12T18:47:00Z

Serveradmin: /* For additional information, please contact Suzanne Leal. */

__NOTITLE__

==Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology==

'''September 14-18, 2026'''
'''Max Delbrück Center (MDC) for Molecular Medicine'''
'''Berlin, Germany'''

This new course is being offered in 2026 at the MDC – '''''Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology''''' – that reflects advances in the field of statistical genetics which have occurred in recent years. The course will be held from September 14-18, 2026. The goal of the course is to teach course participants both the theory and application of statistical methods to provide insight into the etiology of human complex traits using a variety of statistical and bioinformatic methods.

===Course Fees===
The cost of the 5-day course is: Academic Researchers: 975 EUR and Private (for-profit) Companies: 1,950 EUR. The fee covers tuition, the Monday course dinner, and all course-related materials. It does not cover room or board. Housing is available for participants at nearby hotels.

===Topics Covered===
The course curriculum includes:

* Association analysis of qualitative and quantitative traits (rare and common variants)
** Obtained from genotype arrays, imputation, and exome and whole genome sequence data
* Data quality control (genetic and phenotype)
* Linear mixed models (LMM/GLMM)
* Controlling for population admixture, substructure, and confounders
* Gene x gene and gene x environment interactions
* Imputation of variant data
* Pleiotropy, mediation analysis, and Mendelian randomization (MR)
* Heritability estimation, genetic correlations, and polygenic scores (PGS)
* Power and sample size estimation
* Permutation, family-wise error rate (FWER), and false discovery rate (FDR)
* Meta-analysis and fine mapping
* Proteomic-wide association studies (PWAS)

===Computer Exercises===
Hands-on exercises will be conducted using the following programs:

* ANNOVAR
* bcftool
* Fast-LMM
* GCTA
* LD clumping
* LDSC regression
* Mediation
* PLINK
* R
* REGENIE
* TwoSampleMR.

===Instructors===
* '''Suzanne Leal''' (Columbia University)
* '''Michael Nothnagel''' (University of Cologne)

====For additional information, please contact [mailto:suzannemleal@gmail.com Suzanne Leal].====
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/schedules/Schedule_Berlin_GA_Beyond_2026.pdf Course Schedule]
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/applications/Berlin_GA_Beyond_Application_2026.docx Application Form]
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/flyer/Berlin_GA_Beyond_flyer_2026.pdf Course Flyer]

GABeyond2026

2026-01-08T20:00:02Z

Serveradmin: /* Topics Covered */

__NOTITLE__

==Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology==

'''September 14-18, 2026'''
'''Max Delbrück Center (MDC) for Molecular Medicine'''
'''Berlin, Germany'''

This new course is being offered in 2026 at the MDC – '''''Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology''''' – that reflects advances in the field of statistical genetics which have occurred in recent years. The course will be held from September 14-18, 2026. The goal of the course is to teach course participants both the theory and application of statistical methods to provide insight into the etiology of human complex traits using a variety of statistical and bioinformatic methods.

===Course Fees===
The cost of the 5-day course is: Academic Researchers: 975 EUR and Private (for-profit) Companies: 1,950 EUR. The fee covers tuition, the Monday course dinner, and all course-related materials. It does not cover room or board. Housing is available for participants at nearby hotels.

===Topics Covered===
The course curriculum includes:

* Association analysis of qualitative and quantitative traits (rare and common variants)
** Obtained from genotype arrays, imputation, and exome and whole genome sequence data
* Data quality control (genetic and phenotype)
* Linear mixed models (LMM/GLMM)
* Controlling for population admixture, substructure, and confounders
* Gene x gene and gene x environment interactions
* Imputation of variant data
* Pleiotropy, mediation analysis, and Mendelian randomization (MR)
* Heritability estimation, genetic correlations, and polygenic scores (PGS)
* Power and sample size estimation
* Permutation, family-wise error rate (FWER), and false discovery rate (FDR)
* Meta-analysis and fine mapping
* Proteomic-wide association studies (PWAS)

===Computer Exercises===
Hands-on exercises will be conducted using the following programs:

* ANNOVAR
* bcftool
* Fast-LMM
* GCTA
* LD clumping
* LDSC regression
* Mediation
* PLINK
* R
* REGENIE
* TwoSampleMR.

===Instructors===
* '''Suzanne Leal''' (Columbia University)
* '''Michael Nothnagel''' (University of Cologne)

===For additional information, please contact [mailto:suzannemleal@gmail.com Suzanne Leal].===
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/schedules/Schedule_Berlin_GA_Beyond_2026.pdf Course Schedule]
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/applications/Berlin_GA_Beyond_Application_2026.docx Application Form]
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/flyer/Berlin_GA_Beyond_flyer_2026.pdf Course Flyer]

GABeyond2026

2026-01-08T19:59:29Z

Serveradmin: /* For additional information, please contact Suzanne Leal. */

__NOTITLE__

==Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology==

'''September 14-18, 2026'''
'''Max Delbrück Center (MDC) for Molecular Medicine'''
'''Berlin, Germany'''

This new course is being offered in 2026 at the MDC – '''''Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology''''' – that reflects advances in the field of statistical genetics which have occurred in recent years. The course will be held from September 14-18, 2026. The goal of the course is to teach course participants both the theory and application of statistical methods to provide insight into the etiology of human complex traits using a variety of statistical and bioinformatic methods.

===Course Fees===
The cost of the 5-day course is: Academic Researchers: 975 EUR and Private (for-profit) Companies: 1,950 EUR. The fee covers tuition, the Monday course dinner, and all course-related materials. It does not cover room or board. Housing is available for participants at nearby hotels.

===Topics Covered===
The course curriculum includes:

* Association analysis of qualitative and quantitative traits (rare and common variants)
** obtained from genotype arrays, imputation, and exome and whole genome sequence data
* Data quality control (genetic and phenotype)
* Linear mixed models (LMM/GLMM)
* Controlling for population admixture, substructure, and confounders
* Gene x gene and gene x environment interactions
* Imputation of variant data
* Pleiotropy, mediation analysis, and Mendelian randomization (MR)
* Heritability estimation, genetic correlations, and polygenic scores (PGS)
* Power and sample size estimation
* Permutation, family-wise error rate (FWER), and false discovery rate (FDR)
* Meta-analysis and fine mapping
* Proteomic-wide association studies (PWAS)

===Computer Exercises===
Hands-on exercises will be conducted using the following programs:

* ANNOVAR
* bcftool
* Fast-LMM
* GCTA
* LD clumping
* LDSC regression
* Mediation
* PLINK
* R
* REGENIE
* TwoSampleMR.

===Instructors===
* '''Suzanne Leal''' (Columbia University)
* '''Michael Nothnagel''' (University of Cologne)

===For additional information, please contact [mailto:suzannemleal@gmail.com Suzanne Leal].===
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/schedules/Schedule_Berlin_GA_Beyond_2026.pdf Course Schedule]
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/applications/Berlin_GA_Beyond_Application_2026.docx Application Form]
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/flyer/Berlin_GA_Beyond_flyer_2026.pdf Course Flyer]

GABeyond2026

2026-01-08T19:58:43Z

Serveradmin: /* Contact and Registration */

__NOTITLE__

==Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology==

'''September 14-18, 2026'''
'''Max Delbrück Center (MDC) for Molecular Medicine'''
'''Berlin, Germany'''

This new course is being offered in 2026 at the MDC – '''''Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology''''' – that reflects advances in the field of statistical genetics which have occurred in recent years. The course will be held from September 14-18, 2026. The goal of the course is to teach course participants both the theory and application of statistical methods to provide insight into the etiology of human complex traits using a variety of statistical and bioinformatic methods.

===Course Fees===
The cost of the 5-day course is: Academic Researchers: 975 EUR and Private (for-profit) Companies: 1,950 EUR. The fee covers tuition, the Monday course dinner, and all course-related materials. It does not cover room or board. Housing is available for participants at nearby hotels.

===Topics Covered===
The course curriculum includes:

* Association analysis of qualitative and quantitative traits (rare and common variants)
** obtained from genotype arrays, imputation, and exome and whole genome sequence data
* Data quality control (genetic and phenotype)
* Linear mixed models (LMM/GLMM)
* Controlling for population admixture, substructure, and confounders
* Gene x gene and gene x environment interactions
* Imputation of variant data
* Pleiotropy, mediation analysis, and Mendelian randomization (MR)
* Heritability estimation, genetic correlations, and polygenic scores (PGS)
* Power and sample size estimation
* Permutation, family-wise error rate (FWER), and false discovery rate (FDR)
* Meta-analysis and fine mapping
* Proteomic-wide association studies (PWAS)

===Computer Exercises===
Hands-on exercises will be conducted using the following programs:

* ANNOVAR
* bcftool
* Fast-LMM
* GCTA
* LD clumping
* LDSC regression
* Mediation
* PLINK
* R
* REGENIE
* TwoSampleMR.

===Instructors===
* '''Suzanne Leal''' (Columbia University)
* '''Michael Nothnagel''' (University of Cologne)

===For additional information, please contact [mailto:suzannemleal@gmail.com Suzanne Leal].===

* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/schedules/Schedule_Berlin_GA_Beyond_2026.pdf Course Schedule]
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/applications/Berlin_GA_Beyond_Application_2026.docx Application Form]
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/flyer/Berlin_GA_Beyond_flyer_2026.pdf Course Flyer]

GABeyond2026

2026-01-08T19:58:04Z

Serveradmin: /* Topics Covered */

__NOTITLE__

==Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology==

'''September 14-18, 2026'''
'''Max Delbrück Center (MDC) for Molecular Medicine'''
'''Berlin, Germany'''

This new course is being offered in 2026 at the MDC – '''''Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology''''' – that reflects advances in the field of statistical genetics which have occurred in recent years. The course will be held from September 14-18, 2026. The goal of the course is to teach course participants both the theory and application of statistical methods to provide insight into the etiology of human complex traits using a variety of statistical and bioinformatic methods.

===Course Fees===
The cost of the 5-day course is: Academic Researchers: 975 EUR and Private (for-profit) Companies: 1,950 EUR. The fee covers tuition, the Monday course dinner, and all course-related materials. It does not cover room or board. Housing is available for participants at nearby hotels.

===Topics Covered===
The course curriculum includes:

* Association analysis of qualitative and quantitative traits (rare and common variants)
** obtained from genotype arrays, imputation, and exome and whole genome sequence data
* Data quality control (genetic and phenotype)
* Linear mixed models (LMM/GLMM)
* Controlling for population admixture, substructure, and confounders
* Gene x gene and gene x environment interactions
* Imputation of variant data
* Pleiotropy, mediation analysis, and Mendelian randomization (MR)
* Heritability estimation, genetic correlations, and polygenic scores (PGS)
* Power and sample size estimation
* Permutation, family-wise error rate (FWER), and false discovery rate (FDR)
* Meta-analysis and fine mapping
* Proteomic-wide association studies (PWAS)

===Computer Exercises===
Hands-on exercises will be conducted using the following programs:

* ANNOVAR
* bcftool
* Fast-LMM
* GCTA
* LD clumping
* LDSC regression
* Mediation
* PLINK
* R
* REGENIE
* TwoSampleMR.

===Instructors===
* '''Suzanne Leal''' (Columbia University)
* '''Michael Nothnagel''' (University of Cologne)

===Contact and Registration===
For additional information, please contact [mailto:suzannemleal@gmail.com Suzanne Leal].

* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/schedules/Schedule_Berlin_GA_Beyond_2026.pdf Course Schedule]
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/applications/Berlin_GA_Beyond_Application_2026.docx Application Form]
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/flyer/Berlin_GA_Beyond_flyer_2026.pdf Course Flyer]

GABeyond2026

2026-01-08T19:54:33Z

Serveradmin: /* Topics Covered */

__NOTITLE__

==Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology==

'''September 14-18, 2026'''
'''Max Delbrück Center (MDC) for Molecular Medicine'''
'''Berlin, Germany'''

This new course is being offered in 2026 at the MDC – '''''Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology''''' – that reflects advances in the field of statistical genetics which have occurred in recent years. The course will be held from September 14-18, 2026. The goal of the course is to teach course participants both the theory and application of statistical methods to provide insight into the etiology of human complex traits using a variety of statistical and bioinformatic methods.

===Course Fees===
The cost of the 5-day course is: Academic Researchers: 975 EUR and Private (for-profit) Companies: 1,950 EUR. The fee covers tuition, the Monday course dinner, and all course-related materials. It does not cover room or board. Housing is available for participants at nearby hotels.

===Topics Covered===
The course curriculum includes:

* Association analysis of qualitative and quantitative traits (rare and common variants)
* Genotype arrays, imputation, exome, and whole genome sequence data
* Data quality control and linear mixed models (LMM/GLMM)
* Controlling for population admixture, substructure, and confounders
* Gene x gene and gene x environment interactions
* Pleiotropy, mediation analysis, and Mendelian randomization (MR)
* Heritability estimation, genetic correlations, and polygenic scores (PGS)
* Power and sample size estimation
* Permutation, family-wise error rate (FWER), and false discovery rate (FDR)
* Meta-analysis and fine mapping
* Proteomic-wide association studies (PWAS)

===Computer Exercises===
Hands-on exercises will be conducted using the following programs:

* ANNOVAR
* bcftool
* Fast-LMM
* GCTA
* LD clumping
* LDSC regression
* Mediation
* PLINK
* R
* REGENIE
* TwoSampleMR.

===Instructors===
* '''Suzanne Leal''' (Columbia University)
* '''Michael Nothnagel''' (University of Cologne)

===Contact and Registration===
For additional information, please contact [mailto:suzannemleal@gmail.com Suzanne Leal].

* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/schedules/Schedule_Berlin_GA_Beyond_2026.pdf Course Schedule]
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/applications/Berlin_GA_Beyond_Application_2026.docx Application Form]
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/flyer/Berlin_GA_Beyond_flyer_2026.pdf Course Flyer]

GABeyond2026

2026-01-07T23:40:14Z

Serveradmin: /* Course Fees */

__NOTITLE__

==Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology==

'''September 14-18, 2026'''
'''Max Delbrück Center (MDC) for Molecular Medicine'''
'''Berlin, Germany'''

This new course is being offered in 2026 at the MDC – '''''Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology''''' – that reflects advances in the field of statistical genetics which have occurred in recent years. The course will be held from September 14-18, 2026. The goal of the course is to teach course participants both the theory and application of statistical methods to provide insight into the etiology of human complex traits using a variety of statistical and bioinformatic methods.

===Course Fees===
The cost of the 5-day course is: Academic Researchers: 975 EUR and Private (for-profit) Companies: 1,950 EUR. The fee covers tuition, the Monday course dinner, and all course-related materials. It does not cover room or board. Housing is available for participants at nearby hotels.

===Topics Covered===
The course curriculum includes:

* Association analysis of qualitative and quantitative traits (rare and common variants)
* Genotype arrays, imputation, exome, and whole genome sequence data
* Data quality control and linear mixed models (LMM/GLMM)
* Controlling for population admixture, substructure, and confounders
* Gene x gene and gene x environmental interactions
* Pleiotropy, mediation analysis, and Mendelian randomization (MR)
* Heritability estimation, genetic correlations, and polygenic scores (PGS)
* Power and sample size estimation
* Permutation, family-wise error rate (FWER), and false discovery rate (FDR)
* Meta-analysis and fine mapping
* Proteomic-wide association studies (PWAS)

===Computer Exercises===
Hands-on exercises will be conducted using the following programs:

* ANNOVAR
* bcftool
* Fast-LMM
* GCTA
* LD clumping
* LDSC regression
* Mediation
* PLINK
* R
* REGENIE
* TwoSampleMR.

===Instructors===
* '''Suzanne Leal''' (Columbia University)
* '''Michael Nothnagel''' (University of Cologne)

===Contact and Registration===
For additional information, please contact [mailto:suzannemleal@gmail.com Suzanne Leal].

* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/schedules/Schedule_Berlin_GA_Beyond_2026.pdf Course Schedule]
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/applications/Berlin_GA_Beyond_Application_2026.docx Application Form]
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/flyer/Berlin_GA_Beyond_flyer_2026.pdf Course Flyer]

GABeyond2026

2026-01-07T23:39:00Z

Serveradmin: /* Contact and Registration */

__NOTITLE__

==Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology==

'''September 14-18, 2026'''
'''Max Delbrück Center (MDC) for Molecular Medicine'''
'''Berlin, Germany'''

This new course is being offered in 2026 at the MDC – '''''Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology''''' – that reflects advances in the field of statistical genetics which have occurred in recent years. The course will be held from September 14-18, 2026. The goal of the course is to teach course participants both the theory and application of statistical methods to provide insight into the etiology of human complex traits using a variety of statistical and bioinformatic methods.

===Course Fees===
The cost of the 5-day course is: Academic Researchers: 975 EUR and '''P'''rivate (for-profit) Companies: 1,950 EUR. The fee covers tuition, the Monday course dinner, and all course-related materials. It does '''not''' cover room or board. Housing is available for participants at nearby hotels.

===Topics Covered===
The course curriculum includes:

* Association analysis of qualitative and quantitative traits (rare and common variants)
* Genotype arrays, imputation, exome, and whole genome sequence data
* Data quality control and linear mixed models (LMM/GLMM)
* Controlling for population admixture, substructure, and confounders
* Gene x gene and gene x environmental interactions
* Pleiotropy, mediation analysis, and Mendelian randomization (MR)
* Heritability estimation, genetic correlations, and polygenic scores (PGS)
* Power and sample size estimation
* Permutation, family-wise error rate (FWER), and false discovery rate (FDR)
* Meta-analysis and fine mapping
* Proteomic-wide association studies (PWAS)

===Computer Exercises===
Hands-on exercises will be conducted using the following programs:

* ANNOVAR
* bcftool
* Fast-LMM
* GCTA
* LD clumping
* LDSC regression
* Mediation
* PLINK
* R
* REGENIE
* TwoSampleMR.

===Instructors===
* '''Suzanne Leal''' (Columbia University)
* '''Michael Nothnagel''' (University of Cologne)

===Contact and Registration===
For additional information, please contact [mailto:suzannemleal@gmail.com Suzanne Leal].

* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/schedules/Schedule_Berlin_GA_Beyond_2026.pdf Course Schedule]
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/applications/Berlin_GA_Beyond_Application_2026.docx Application Form]
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/flyer/Berlin_GA_Beyond_flyer_2026.pdf Course Flyer]

GABeyond2026

2026-01-07T23:38:02Z

Serveradmin:

__NOTITLE__

==Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology==

'''September 14-18, 2026'''
'''Max Delbrück Center (MDC) for Molecular Medicine'''
'''Berlin, Germany'''

This new course is being offered in 2026 at the MDC – '''''Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology''''' – that reflects advances in the field of statistical genetics which have occurred in recent years. The course will be held from September 14-18, 2026. The goal of the course is to teach course participants both the theory and application of statistical methods to provide insight into the etiology of human complex traits using a variety of statistical and bioinformatic methods.

===Course Fees===
The cost of the 5-day course is: Academic Researchers: 975 EUR and '''P'''rivate (for-profit) Companies: 1,950 EUR. The fee covers tuition, the Monday course dinner, and all course-related materials. It does '''not''' cover room or board. Housing is available for participants at nearby hotels.

===Topics Covered===
The course curriculum includes:

* Association analysis of qualitative and quantitative traits (rare and common variants)
* Genotype arrays, imputation, exome, and whole genome sequence data
* Data quality control and linear mixed models (LMM/GLMM)
* Controlling for population admixture, substructure, and confounders
* Gene x gene and gene x environmental interactions
* Pleiotropy, mediation analysis, and Mendelian randomization (MR)
* Heritability estimation, genetic correlations, and polygenic scores (PGS)
* Power and sample size estimation
* Permutation, family-wise error rate (FWER), and false discovery rate (FDR)
* Meta-analysis and fine mapping
* Proteomic-wide association studies (PWAS)

===Computer Exercises===
Hands-on exercises will be conducted using the following programs:

* ANNOVAR
* bcftool
* Fast-LMM
* GCTA
* LD clumping
* LDSC regression
* Mediation
* PLINK
* R
* REGENIE
* TwoSampleMR.

===Instructors===
* '''Suzanne Leal''' (Columbia University)
* '''Michael Nothnagel''' (University of Cologne)

===Contact and Registration===
For additional information, please contact [mailto:suzannemleal@gmail.com Suzanne Leal].

* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/schedules/Schedule_Berlin_GA_Beyond_2026.pdf Course Schedule]
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/schedules/Berlin_GA_Beyond_Application_2026.docx Application Form]
* [https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/schedules/Berlin_GA_Beyond_flyer_2026.pdf Course Flyer]

GABeyond2026

2026-01-07T23:21:55Z

Serveradmin:

__NOTITLE__

==Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology==

'''September 14-18, 2026'''
'''Max Delbrück Center (MDC) for Molecular Medicine'''
'''Berlin, Germany'''

This new course is being offered in 2026 at the MDC – '''''Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology''''' – that reflects advances in the field of statistical genetics which have occurred in recent years. The course will be held from September 14-18, 2026. The goal of the course is to teach course participants both the theory and application of statistical methods to provide insight into the etiology of human complex traits using a variety of statistical and bioinformatic methods.

===Course Fees===
The cost of the 5-day course is: Academic Researchers: 975 EUR and '''P'''rivate (for-profit) Companies: 1,950 EUR. The fee covers tuition, the Monday course dinner, and all course-related materials. It does '''not''' cover room or board. Housing is available for participants at nearby hotels.

===Topics Covered===
The course curriculum includes:

* Association analysis of qualitative and quantitative traits (rare and common variants)
* Genotype arrays, imputation, exome, and whole genome sequence data
* Data quality control and linear mixed models (LMM/GLMM)
* Controlling for population admixture, substructure, and confounders
* Gene x gene and gene x environmental interactions
* Pleiotropy, mediation analysis, and Mendelian randomization (MR)
* Heritability estimation, genetic correlations, and polygenic scores (PGS)
* Power and sample size estimation
* Permutation, family-wise error rate (FWER), and false discovery rate (FDR)
* Meta-analysis and fine mapping
* Proteomic-wide association studies (PWAS)

===Computer Exercises===
Hands-on exercises will be conducted using the following programs:

* ANNOVAR
* bcftool
* Fast-LMM
* GCTA
* LD clumping
* LDSC regression
* Mediation
* PLINK
* R
* REGENIE
* TwoSampleMR.

===Instructors===
* '''Suzanne Leal''' (Columbia University)
* '''Michael Nothnagel''' (University of Cologne)

===Contact and Registration===
For additional information, please contact [mailto:suzannemleal@gmail.com Suzanne Leal].

* [https://statgen.us/files/2024/09/schedule_berlin_genetic_association_course_Sept_2024.pdf Course Schedule]
* [https://statgen.us/files/2024/09/Berlin_Genet_Association_Course_Application_2024.html Application Form]
* [https://statgen.us/files/2024/09/Berlin_genetic_association_flyer_2024.pdf Course Flyer]

GABeyond2026

2026-01-07T23:21:04Z

Serveradmin: /* Genetic Association and Beyond:Statistical Methods to Elucidate Complex Trait Etiology */

==Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology==
'''September 14-18, 2026'''
'''Max Delbrück Center (MDC) for Molecular Medicine'''
'''Berlin, Germany'''

This new course is being offered in 2026 at the MDC – '''''Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology''''' – that reflects advances in the field of statistical genetics which have occurred in recent years. The course will be held from September 14-18, 2026. The goal of the course is to teach course participants both the theory and application of statistical methods to provide insight into the etiology of human complex traits using a variety of statistical and bioinformatic methods.

===Course Fees===
The cost of the 5-day course is: Academic Researchers: 975 EUR and '''P'''rivate (for-profit) Companies: 1,950 EUR. The fee covers tuition, the Monday course dinner, and all course-related materials. It does '''not''' cover room or board. Housing is available for participants at nearby hotels.

===Topics Covered===
The course curriculum includes:

* Association analysis of qualitative and quantitative traits (rare and common variants)
* Genotype arrays, imputation, exome, and whole genome sequence data
* Data quality control and linear mixed models (LMM/GLMM)
* Controlling for population admixture, substructure, and confounders
* Gene x gene and gene x environmental interactions
* Pleiotropy, mediation analysis, and Mendelian randomization (MR)
* Heritability estimation, genetic correlations, and polygenic scores (PGS)
* Power and sample size estimation
* Permutation, family-wise error rate (FWER), and false discovery rate (FDR)
* Meta-analysis and fine mapping
* Proteomic-wide association studies (PWAS)

===Computer Exercises===
Hands-on exercises will be conducted using the following programs:

* ANNOVAR
* bcftool
* Fast-LMM
* GCTA
* LD clumping
* LDSC regression
* Mediation
* PLINK
* R
* REGENIE
* TwoSampleMR.

===Instructors===
* '''Suzanne Leal''' (Columbia University)
* '''Michael Nothnagel''' (University of Cologne)

===Contact and Registration===
For additional information, please contact [mailto:suzannemleal@gmail.com Suzanne Leal].

* [https://statgen.us/files/2024/09/schedule_berlin_genetic_association_course_Sept_2024.pdf Course Schedule]
* [https://statgen.us/files/2024/09/Berlin_Genet_Association_Course_Application_2024.html Application Form]
* [https://statgen.us/files/2024/09/Berlin_genetic_association_flyer_2024.pdf Course Flyer]

Main Page

2026-01-07T23:20:56Z

Serveradmin: /* Statistical Genetics Courses */

__NOTOC__

==Statistical Genetics Training Resources==
We are an international group of statistical geneticists who wish to make training resources available to the genetics community. We offer tutorials for a variety of analysis tools/software. We also offer courses on a variety of topics related to analysis of human genetic data.

===Our group===
* Heather Cordell, Ph.D. (Newcastle University)
* Andrew DeWan, Ph.D. (Yale University)
* Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University)
* Michael Nothnagel, Ph.D. (University of Cologne)
* Gao T. Wang, Ph.D. (Columbia University)

Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses

For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions

==Statistical Genetics Courses==
'''[[Advgenemap2026|Advanced Gene Mapping]]''' June 1-5, 2026 (tentative) The Rockefeller University, New York, USA

'''[[GABeyond2026|Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology]]''' September 14-18, 2026 The Max Delbrück Center, Berlin, Germany

 
[[Previous_Courses|Previous Course Pages]]

==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#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[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#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#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#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#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]

Main Page

2026-01-07T23:20:52Z

Serveradmin: /* Statistical Genetics Courses */

__NOTOC__

==Statistical Genetics Training Resources==
We are an international group of statistical geneticists who wish to make training resources available to the genetics community. We offer tutorials for a variety of analysis tools/software. We also offer courses on a variety of topics related to analysis of human genetic data.

===Our group===
* Heather Cordell, Ph.D. (Newcastle University)
* Andrew DeWan, Ph.D. (Yale University)
* Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University)
* Michael Nothnagel, Ph.D. (University of Cologne)
* Gao T. Wang, Ph.D. (Columbia University)

Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses

For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions

==Statistical Genetics Courses==
'''[[Advgenemap2026|Advanced Gene Mapping]]''' June 1-5, 2026 (tentative) The Rockefeller University, New York, USA

'''[[GABeyond2026|Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology]]''' September 14-18, 2026 The Max Delbrück Center, Berlin, Germany

 
[[Previous_Courses|Previous Course Pages]]

==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#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[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#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#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#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#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]

Main Page

2026-01-07T23:20:48Z

Serveradmin: /* Statistical Genetics Courses */

__NOTOC__

==Statistical Genetics Training Resources==
We are an international group of statistical geneticists who wish to make training resources available to the genetics community. We offer tutorials for a variety of analysis tools/software. We also offer courses on a variety of topics related to analysis of human genetic data.

===Our group===
* Heather Cordell, Ph.D. (Newcastle University)
* Andrew DeWan, Ph.D. (Yale University)
* Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University)
* Michael Nothnagel, Ph.D. (University of Cologne)
* Gao T. Wang, Ph.D. (Columbia University)

Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses

For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions

==Statistical Genetics Courses==
'''[[Advgenemap2026|Advanced Gene Mapping]]''' June 1-5, 2026 (tentative) The Rockefeller University, New York, USA

'''[[GABeyond2026|Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology]]''' September 14-18, 2026 The Max Delbrück Center, Berlin, Germany

 
[[Previous_Courses|Previous Course Pages]]

==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#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[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#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#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#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#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]

Main Page

2026-01-07T23:20:45Z

Serveradmin: /* Statistical Genetics Courses */

__NOTOC__

==Statistical Genetics Training Resources==
We are an international group of statistical geneticists who wish to make training resources available to the genetics community. We offer tutorials for a variety of analysis tools/software. We also offer courses on a variety of topics related to analysis of human genetic data.

===Our group===
* Heather Cordell, Ph.D. (Newcastle University)
* Andrew DeWan, Ph.D. (Yale University)
* Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University)
* Michael Nothnagel, Ph.D. (University of Cologne)
* Gao T. Wang, Ph.D. (Columbia University)

Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses

For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions

==Statistical Genetics Courses==
'''[[Advgenemap2026|Advanced Gene Mapping]]''' June 1-5, 2026 (tentative) The Rockefeller University, New York, USA

'''[[GABeyond2026|Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology]]''' September 14-18, 2026 The Max Delbrück Center, Berlin, Germany

 
[[Previous_Courses|Previous Course Pages]]

==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#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[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#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#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#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#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]

GABeyond2026

2026-01-07T23:20:42Z

Serveradmin:

==Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology==
'''September 14-18, 2026'''
'''Max Delbrück Center (MDC) for Molecular Medicine'''
'''Berlin, Germany'''

This new course is being offered in 2026 at the MDC – '''''Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology''''' – that reflects advances in the field of statistical genetics which have occurred in recent years. The course will be held from September 14-18, 2026. The goal of the course is to teach course participants both the theory and application of statistical methods to provide insight into the etiology of human complex traits using a variety of statistical and bioinformatic methods.

===Course Fees===
The cost of the 5-day course is: Academic Researchers: 975 EUR and '''P'''rivate (for-profit) Companies: 1,950 EUR. The fee covers tuition, the Monday course dinner, and all course-related materials. It does '''not''' cover room or board. Housing is available for participants at nearby hotels.

===Topics Covered===
The course curriculum includes:

* Association analysis of qualitative and quantitative traits (rare and common variants)
* Genotype arrays, imputation, exome, and whole genome sequence data
* Data quality control and linear mixed models (LMM/GLMM)
* Controlling for population admixture, substructure, and confounders
* Gene x gene and gene x environmental interactions
* Pleiotropy, mediation analysis, and Mendelian randomization (MR)
* Heritability estimation, genetic correlations, and polygenic scores (PGS)
* Power and sample size estimation
* Permutation, family-wise error rate (FWER), and false discovery rate (FDR)
* Meta-analysis and fine mapping
* Proteomic-wide association studies (PWAS)

===Computer Exercises===
Hands-on exercises will be conducted using the following programs:

* ANNOVAR
* bcftool
* Fast-LMM
* GCTA
* LD clumping
* LDSC regression
* Mediation
* PLINK
* R
* REGENIE
* TwoSampleMR.

===Instructors===
* '''Suzanne Leal''' (Columbia University)
* '''Michael Nothnagel''' (University of Cologne)

===Contact and Registration===
For additional information, please contact [mailto:suzannemleal@gmail.com Suzanne Leal].

* [https://statgen.us/files/2024/09/schedule_berlin_genetic_association_course_Sept_2024.pdf Course Schedule]
* [https://statgen.us/files/2024/09/Berlin_Genet_Association_Course_Application_2024.html Application Form]
* [https://statgen.us/files/2024/09/Berlin_genetic_association_flyer_2024.pdf Course Flyer]

Main Page

2026-01-07T23:20:41Z

Serveradmin: /* Statistical Genetics Courses */

__NOTOC__

==Statistical Genetics Training Resources==
We are an international group of statistical geneticists who wish to make training resources available to the genetics community. We offer tutorials for a variety of analysis tools/software. We also offer courses on a variety of topics related to analysis of human genetic data.

===Our group===
* Heather Cordell, Ph.D. (Newcastle University)
* Andrew DeWan, Ph.D. (Yale University)
* Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University)
* Michael Nothnagel, Ph.D. (University of Cologne)
* Gao T. Wang, Ph.D. (Columbia University)

Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses

For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions

==Statistical Genetics Courses==
'''[[Advgenemap2026|Advanced Gene Mapping]]''' June 1-5, 2026 (tentative) The Rockefeller University, New York, USA

'''[[GABeyond2026|Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology]]''' September 14-18, 2026 The Max Delbrück Center, Berlin, Germany

 
[[Previous_Courses|Previous Course Pages]]

==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#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[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#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#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#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#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]

Main Page

2026-01-07T23:20:37Z

Serveradmin: /* Statistical Genetics Courses */

__NOTOC__

==Statistical Genetics Training Resources==
We are an international group of statistical geneticists who wish to make training resources available to the genetics community. We offer tutorials for a variety of analysis tools/software. We also offer courses on a variety of topics related to analysis of human genetic data.

===Our group===
* Heather Cordell, Ph.D. (Newcastle University)
* Andrew DeWan, Ph.D. (Yale University)
* Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University)
* Michael Nothnagel, Ph.D. (University of Cologne)
* Gao T. Wang, Ph.D. (Columbia University)

Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses

For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions

==Statistical Genetics Courses==
'''[[Advgenemap2026|Advanced Gene Mapping]]''' June 1-5, 2026 (tentative) The Rockefeller University, New York, USA

'''[[GABeyond2026|Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology]]''' September 14-18, 2026 The Max Delbrück Center, Berlin, Germany

 
[[Previous_Courses|Previous Course Pages]]

==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#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[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#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#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#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#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]

GABeyond2026

2026-01-07T23:19:21Z

Serveradmin: Created page with "==Genetic Association and Beyond:== ==Statistical Methods to Elucidate Complex Trait Etiology== '''September 14-18, 2026''' '''Max Delbrück Center (MDC) for Molecular Medicin..."

==Genetic Association and Beyond:==
==Statistical Methods to Elucidate Complex Trait Etiology==
'''September 14-18, 2026'''
'''Max Delbrück Center (MDC) for Molecular Medicine'''
'''Berlin, Germany'''

This new course is being offered in 2026 at the MDC – '''''Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology''''' – that reflects advances in the field of statistical genetics which have occurred in recent years. The course will be held from September 14-18, 2026. The goal of the course is to teach course participants both the theory and application of statistical methods to provide insight into the etiology of human complex traits using a variety of statistical and bioinformatic methods.

===Course Fees===
The cost of the 5-day course is: Academic Researchers: 975 EUR and '''P'''rivate (for-profit) Companies: 1,950 EUR. The fee covers tuition, the Monday course dinner, and all course-related materials. It does '''not''' cover room or board. Housing is available for participants at nearby hotels.

===Topics Covered===
The course curriculum includes:

* Association analysis of qualitative and quantitative traits (rare and common variants)
* Genotype arrays, imputation, exome, and whole genome sequence data
* Data quality control and linear mixed models (LMM/GLMM)
* Controlling for population admixture, substructure, and confounders
* Gene x gene and gene x environmental interactions
* Pleiotropy, mediation analysis, and Mendelian randomization (MR)
* Heritability estimation, genetic correlations, and polygenic scores (PGS)
* Power and sample size estimation
* Permutation, family-wise error rate (FWER), and false discovery rate (FDR)
* Meta-analysis and fine mapping
* Proteomic-wide association studies (PWAS)

===Computer Exercises===
Hands-on exercises will be conducted using the following programs:

* ANNOVAR
* bcftool
* Fast-LMM
* GCTA
* LD clumping
* LDSC regression
* Mediation
* PLINK
* R
* REGENIE
* TwoSampleMR.

===Instructors===
* '''Suzanne Leal''' (Columbia University)
* '''Michael Nothnagel''' (University of Cologne)

===Contact and Registration===
For additional information, please contact [mailto:suzannemleal@gmail.com Suzanne Leal].

* [https://statgen.us/files/2024/09/schedule_berlin_genetic_association_course_Sept_2024.pdf Course Schedule]
* [https://statgen.us/files/2024/09/Berlin_Genet_Association_Course_Application_2024.html Application Form]
* [https://statgen.us/files/2024/09/Berlin_genetic_association_flyer_2024.pdf Course Flyer]

GenAssocStatMeth2026

2026-01-07T23:11:23Z

Serveradmin: Created page with " {{Note|The following information describes the "Genetic Association and Beyond" course scheduled for September 2026.}} == Genetic Association and Beyond: Statistical Methods..."

{{Note|The following information describes the "Genetic Association and Beyond" course scheduled for September 2026.}}

== Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology ==

'''September 14-18, 2026'''
'''Max Delbrück Center (MDC) for Molecular Medicine'''
'''Berlin, Germany'''

----

This new course is being offered in 2026 at the MDC – '''''Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology''''' – that reflects advances in the field of statistical genetics which have occurred in recent years. The course will be held from September 14-18, 2026. The goal of the course is to teach course participants both the theory and application of statistical methods to provide insight into the etiology of human complex traits using a variety of statistical and bioinformatic methods.

=== Course Fees ===
The cost of the 5-day course is:
* '''Academic Researchers:''' 975 EUR
* '''Private (for-profit) Companies:''' 1,950 EUR

The fee covers tuition, the Monday course dinner, and all course-related materials. It does '''not''' cover room or board. Housing is available for participants at nearby hotels.

=== Topics Covered ===
The course curriculum includes:
* Association analysis of qualitative and quantitative traits (rare and common variants)
* Genotype arrays, imputation, exome, and whole genome sequence data
* Data quality control and linear mixed models (LMM/GLMM)
* Controlling for population admixture, substructure, and confounders
* Gene x gene and gene x environmental interactions
* Pleiotropy, mediation analysis, and Mendelian randomization (MR)
* Heritability estimation, genetic correlations, and polygenic scores (PGS)
* Power and sample size estimation
* Permutation, family-wise error rate (FWER), and false discovery rate (FDR)
* Meta-analysis and fine mapping
* Proteomic-wide association studies (PWAS)

=== Computer Exercises ===
Hands-on exercises will be conducted using the following programs:
* ANNOVAR, bcftools, Fast-LMM, GCTA, LD clumping, LDSC regression, mediation, PLINK, R, REGENIE, and TwoSampleMR.

=== Instructors ===
* '''Suzanne Leal''' (Columbia University)
* '''Michael Nothnagel''' (University of Cologne)

=== Contact and Registration ===
For additional information, please contact [mailto:suzannemleal@gmail.com Suzanne Leal].

* [https://statgen.us/files/2024/09/schedule_berlin_genetic_association_course_Sept_2024.pdf Course Schedule]
* [https://statgen.us/files/2024/09/Berlin_Genet_Association_Course_Application_2024.html Application Form]
* [https://statgen.us/files/2024/09/Berlin_genetic_association_flyer_2024.pdf Course Flyer]

Main Page

2025-12-31T03:57:03Z

Serveradmin: /* Statistical Genetics Courses */

__NOTOC__

==Statistical Genetics Training Resources==
We are an international group of statistical geneticists who wish to make training resources available to the genetics community. We offer tutorials for a variety of analysis tools/software. We also offer courses on a variety of topics related to analysis of human genetic data.

===Our group===
* Heather Cordell, Ph.D. (Newcastle University)
* Andrew DeWan, Ph.D. (Yale University)
* Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University)
* Michael Nothnagel, Ph.D. (University of Cologne)
* Gao T. Wang, Ph.D. (Columbia University)

Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses

For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions

==Statistical Genetics Courses==

'''[[Advgenemap2026|Advanced Gene Mapping]]''' June 1-5, 2026 (tentative) The Rockefeller University, New York, USA

'''[[GenAssocStatMeth2026|Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology]]''' September 14-18, 2026 The Max Delbrück Center, Berlin, Germany

 
[[Previous_Courses|Previous Course Pages]]

==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#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[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#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#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#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#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]

Main Page

2025-12-31T03:56:59Z

Serveradmin: /* Statistical Genetics Courses */

__NOTOC__

==Statistical Genetics Training Resources==
We are an international group of statistical geneticists who wish to make training resources available to the genetics community. We offer tutorials for a variety of analysis tools/software. We also offer courses on a variety of topics related to analysis of human genetic data.

===Our group===
* Heather Cordell, Ph.D. (Newcastle University)
* Andrew DeWan, Ph.D. (Yale University)
* Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University)
* Michael Nothnagel, Ph.D. (University of Cologne)
* Gao T. Wang, Ph.D. (Columbia University)

Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses

For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions

==Statistical Genetics Courses==

'''[[Advgenemap2026|Advanced Gene Mapping]]''' June 1-5, 2026 (tentative) The Rockefeller University, New York, USA

'''[[GenAssocStatMeth2026|Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology]]''' September 14-18, 2026 The Max Delbrück Center, Berlin, Germany

 
[[Previous_Courses|Previous Course Pages]]

==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#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[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#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#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#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#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]

Main Page

2025-12-31T03:56:55Z

Serveradmin: /* Statistical Genetics Courses */

__NOTOC__

==Statistical Genetics Training Resources==
We are an international group of statistical geneticists who wish to make training resources available to the genetics community. We offer tutorials for a variety of analysis tools/software. We also offer courses on a variety of topics related to analysis of human genetic data.

===Our group===
* Heather Cordell, Ph.D. (Newcastle University)
* Andrew DeWan, Ph.D. (Yale University)
* Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University)
* Michael Nothnagel, Ph.D. (University of Cologne)
* Gao T. Wang, Ph.D. (Columbia University)

Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses

For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions

==Statistical Genetics Courses==

'''[[Advgenemap2026|Advanced Gene Mapping]]''' June 1-5, 2026 (tentative) The Rockefeller University, New York, USA

'''[[GenAssocStatMeth2026|Genetic Association and Beyond: Statistical Methods to Elucidate Complex Trait Etiology]]''' September 14-18, 2026 The Max Delbrück Center, Berlin, Germany

 
[[Previous_Courses|Previous Course Pages]]

==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#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[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#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#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#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#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]

Main Page

2025-12-29T16:41:26Z

Serveradmin: /* Statistical Genetics Courses */

__NOTOC__

==Statistical Genetics Training Resources==
We are an international group of statistical geneticists who wish to make training resources available to the genetics community. We offer tutorials for a variety of analysis tools/software. We also offer courses on a variety of topics related to analysis of human genetic data.

===Our group===
* Heather Cordell, Ph.D. (Newcastle University)
* Andrew DeWan, Ph.D. (Yale University)
* Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University)
* Michael Nothnagel, Ph.D. (University of Cologne)
* Gao T. Wang, Ph.D. (Columbia University)

Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses

For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions

==Statistical Genetics Courses==

'''[[Advgenemap2026|Advanced Gene Mapping]]''' June 1-5, 2026 (tentative) The Rockefeller University, New York, USA

'''[[GenAssocStatMeth2026|Genetic Association Analysis and Other Statistical Methods Course
With Application to Complex Traits]]''' September 14-18, 2026 The Max Delbrück Center, Berlin, Germany

 
[[Previous_Courses|Previous Course Pages]]

==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#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[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#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#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#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#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]

Main Page

2025-12-29T16:41:21Z

Serveradmin: /* Statistical Genetics Courses */

__NOTOC__

==Statistical Genetics Training Resources==
We are an international group of statistical geneticists who wish to make training resources available to the genetics community. We offer tutorials for a variety of analysis tools/software. We also offer courses on a variety of topics related to analysis of human genetic data.

===Our group===
* Heather Cordell, Ph.D. (Newcastle University)
* Andrew DeWan, Ph.D. (Yale University)
* Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University)
* Michael Nothnagel, Ph.D. (University of Cologne)
* Gao T. Wang, Ph.D. (Columbia University)

Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses

For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions

==Statistical Genetics Courses==

'''[[Advgenemap2026|Advanced Gene Mapping]]''' June 1-5, 2026 (tentative) The Rockefeller University, New York, USA

'''[[GenAssocStatMeth2026|Genetic Association Analysis and Other Statistical Methods Course
With Application to Complex Traits]]''' September 14-18, 2026 The Max Delbrück Center, Berlin, Germany

 
[[Previous_Courses|Previous Course Pages]]

==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#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[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#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#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#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#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]

Main Page

2025-12-29T16:41:17Z

Serveradmin: /* Statistical Genetics Courses */

__NOTOC__

==Statistical Genetics Training Resources==
We are an international group of statistical geneticists who wish to make training resources available to the genetics community. We offer tutorials for a variety of analysis tools/software. We also offer courses on a variety of topics related to analysis of human genetic data.

===Our group===
* Heather Cordell, Ph.D. (Newcastle University)
* Andrew DeWan, Ph.D. (Yale University)
* Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University)
* Michael Nothnagel, Ph.D. (University of Cologne)
* Gao T. Wang, Ph.D. (Columbia University)

Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses

For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions

==Statistical Genetics Courses==

'''[[Advgenemap2026|Advanced Gene Mapping]]''' June 1-5, 2026 (tentative) The Rockefeller University, New York, USA

'''[[GenAssocStatMeth2026|Genetic Association Analysis and Other Statistical Methods Course
With Application to Complex Traits]]''' September 14-18, 2026 The Max Delbrück Center, Berlin, Germany

 
[[Previous_Courses|Previous Course Pages]]

==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#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[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#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#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#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#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]

Main Page

2025-12-29T16:41:12Z

Serveradmin: /* Statistical Genetics Courses */

__NOTOC__

==Statistical Genetics Training Resources==
We are an international group of statistical geneticists who wish to make training resources available to the genetics community. We offer tutorials for a variety of analysis tools/software. We also offer courses on a variety of topics related to analysis of human genetic data.

===Our group===
* Heather Cordell, Ph.D. (Newcastle University)
* Andrew DeWan, Ph.D. (Yale University)
* Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University)
* Michael Nothnagel, Ph.D. (University of Cologne)
* Gao T. Wang, Ph.D. (Columbia University)

Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses

For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions

==Statistical Genetics Courses==

'''[[Advgenemap2026|Advanced Gene Mapping]]''' June 1-5, 2026 (tentative) The Rockefeller University, New York, USA

'''[[GenAssocStatMeth2026|Genetic Association Analysis and Other Statistical Methods Course
With Application to Complex Traits]]''' September 14-18, 2026 The Max Delbrück Center, Berlin, Germany

 
[[Previous_Courses|Previous Course Pages]]

==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#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[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#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#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#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#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]

Main Page

2025-12-29T16:41:08Z

Serveradmin: /* Statistical Genetics Courses */

__NOTOC__

==Statistical Genetics Training Resources==
We are an international group of statistical geneticists who wish to make training resources available to the genetics community. We offer tutorials for a variety of analysis tools/software. We also offer courses on a variety of topics related to analysis of human genetic data.

===Our group===
* Heather Cordell, Ph.D. (Newcastle University)
* Andrew DeWan, Ph.D. (Yale University)
* Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University)
* Michael Nothnagel, Ph.D. (University of Cologne)
* Gao T. Wang, Ph.D. (Columbia University)

Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses

For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions

==Statistical Genetics Courses==

'''[[Advgenemap2026|Advanced Gene Mapping]]''' June 1-5, 2026 (tentative) The Rockefeller University, New York, USA

'''[[GenAssocStatMeth2026|Genetic Association Analysis and Other Statistical Methods Course
With Application to Complex Traits]]''' September 14-18, 2026 The Max Delbrück Center, Berlin, Germany

 
[[Previous_Courses|Previous Course Pages]]

==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#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[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#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#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#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#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]

Main Page

2025-12-29T16:39:56Z

Serveradmin: /* Statistical Genetics Courses */

__NOTOC__

==Statistical Genetics Training Resources==
We are an international group of statistical geneticists who wish to make training resources available to the genetics community. We offer tutorials for a variety of analysis tools/software. We also offer courses on a variety of topics related to analysis of human genetic data.

===Our group===
* Heather Cordell, Ph.D. (Newcastle University)
* Andrew DeWan, Ph.D. (Yale University)
* Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University)
* Michael Nothnagel, Ph.D. (University of Cologne)
* Gao T. Wang, Ph.D. (Columbia University)

Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses

For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions

==Statistical Genetics Courses==

'''[[Advgenemap2026|Advanced Gene Mapping]]''' June 1-5, 2026 (tentative) The Rockefeller University, New York, USA

'''[[GenAssocStatMeth2026|Genetic Association Analysis and Other Statistical Methods Course
With Application to Complex Traits]]''' September 14-18, 2026br />The Max Delbrück Center, Berlin, Germany

 
[[Previous_Courses|Previous Course Pages]]

==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#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[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#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#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#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#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]

Main Page

2025-12-11T16:09:43Z

Serveradmin: /* Statistical Genetics Courses */

__NOTOC__

==Statistical Genetics Training Resources==
We are an international group of statistical geneticists who wish to make training resources available to the genetics community. We offer tutorials for a variety of analysis tools/software. We also offer courses on a variety of topics related to analysis of human genetic data.

===Our group===
* Heather Cordell, Ph.D. (Newcastle University)
* Andrew DeWan, Ph.D. (Yale University)
* Suzanne M. Leal, Ph.D. (Columbia University and Rockefeller University)
* Michael Nothnagel, Ph.D. (University of Cologne)
* Gao T. Wang, Ph.D. (Columbia University)

Material on this site are open source and can be found on GitHub at https://github.com/statgenetics/statgen-courses

For questions concerning material on this site please raise them at the Discussion forum curated by our team, https://github.com/statgenetics/statgen-courses/discussions

==Statistical Genetics Courses==

'''[[Advgenemap2026|Advanced Gene Mapping]]''' June 1-5, 2026 (tentative) The Rockefeller University, New York, USA
 
[[Previous_Courses|Previous Course Pages]]

==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#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[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#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#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#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#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]

Advgenemap2026

2025-12-11T16:04:52Z

Serveradmin: Created page with "__NOTITLE__ ==Advanced Gene Mapping Course== The Rockefeller University, New York Welch - The Great Hall Monday thro..."

__NOTITLE__

==Advanced Gene Mapping Course==
The Rockefeller University, New York 
Welch - The Great Hall 
Monday through Friday, June 1-5, 2026 (tentative)

==General Information==
An Advanced Gene Mapping course will be held in New York from Monday through Friday, June 1-5, 2026 (tentative). The cost of the 5-day course is $100 for student, academic, and government researchers and $2,500 for researchers working in industry. This fee covers tuition and course-related expenses (cloud computing, etc.).

The course emphasizes analyzing sequence and other omics data to elucidate the genetic etiology of complex human disease traits. Topics will include data quality control of sequence and other types of data; single variant and aggregate rare variant association analysis of whole-genome data (genotype, sequence, and imputed) for qualitative and quantitative traits (population and family data); controlling for population admixture and substructure; linear mixed models (LMM) and generalized LMM (GLMM); meta-analysis; sample size estimation, and power calculations; detecting gene x gene and gene x environmental interactions; heritability estimation; transcriptome-wide association studies (TWAS); analysis of RNA-Seq data; eQTL mapping; elucidating pleiotropy; functional prediction and variant annotation; estimation of polygenic risk scores; Mendelian randomization; mediation analysis; LDclumping and fine mapping. As mandated by the NIH there will also be a special session on responsible conduct of research that will include sessions on conflict of interest, research ethics, data management (security), and ethical use of human research subjects.

A variety of freely available software will be used to perform the practical exercises, due to differences in their functionality. FaST-LMM, GCTA, REGENIE will be implemented to analyze population- and family data by applying GLMM and LMM. PLINK will be used to perform data quality control and association analysis controlling for population admixture and substructures using principal component analysis (PCA) and multidimensional scaling (MDS). VCFtools and ANNOVAR will be used to perform data quality control and annotation of sequence data and REGENIE to perform single variant and rare variant aggregate association analysis. Gene x gene and gene x environmental interactions will be tested using PLINK and CASSI. Mediation analysis will be performed using Multiphen and R to distinguish between biological, mediated, and spurious pleiotropy. To make inferences on causality, Mendelian randomization will be performed using MRbase and R. MR-JTI will be used to perform TWAS analysis. Estimation of polygenic risk scores will be performed using LDpred2. SuSiE and mvSuSie will be used for fine mapping to aid in detecting causal susceptibility variants. A variety of tools will be used to perform analytical and empirical power analysis for single and rare variant aggregate tests.

==Course Instructors==
The instructors for the course are Heather Cordell (University of Newcastle), Andrew DeWan (Yale University), Suzanne Leal (The Rockefeller University & Columbia University), Shamil Sunyaev (Harvard University) and Gao Wang (Columbia University). TBN (HRP Consulting Group) will lecture on ethics and the regulation of human subject research. A special guest lecture will be given by Jurg Ott (The Rockefeller University).

==Additional Information==
The maximum number of participants for this course is 34.

The course is wheelchair accessible. All disabilities will be accommodated. Handicapped individuals are encouraged to apply.

Travel stipends of up to $1,200 each are available. Eligibility requirements are: (1) sufficient background and practical experience in statistical analysis of genetic data, and (2) demonstrated financial need. Preference for stipends will be given to pre-doctoral students and postdoctoral researchers. To apply for such a stipend, please attach a letter of request and enclose a letter of reference and proof of student or postdoctoral status.

Knowledge genetic association analysis, genetic epidemiology, and/or statistical genetics are screening criteria for the selection of participants. Please submit a copy of your CV with your application as well as a letter describing your expertise/experience in detail, e.g., research and training in statistical genetics or related fields. We may contact you personally to discuss your application. If you do not have experience using Unix/LINUX it is highly beneficial to obtain this knowledge before the start of the course.

The course is supported by generous funding from the National Human Genome Research Institute.

For additional information contact the course organizer [mailto:suzannemleal@gmail.com?subject=Rockefeller%20Advanced%20Gene%20Mapping%20Course%202023 Suzanne Leal]:

email: [mailto:suzannemleal@gmail.com suzannemleal@gmail.com] or [mailto:sml3@cumc.columbia.edu sml3@cumc.columbia.edu]

Previous Courses

2025-11-29T21:19:00Z

Serveradmin:

==[[CourseExerciseScripts|Course Exercise Commands]]==

==2025 Courses==
* [[Advgenemap2025|Advanced Gene Mapping]]
* [[ComplexNGS2025|Genetic Association Course]]

==2024 Courses==
* [[Advgenemap2024|Advanced Gene Mapping]]
* [[Genassoc2024|Genetic Association Course]]

==2023 Courses==
* [[Advgenemap2023|Advanced Gene Mapping]]
* [[ComplexNGS2023|Complex Trait Analysis of Next Generation Sequence Data]]

==2022 Courses==
* [[Advgenemap2022|Advanced Gene Mapping]] (Oneline due to COVID)
* [[Genassoc2022|Genetic Association]]
* [[AdvgenemapNov2022|Advanced Gene Mapping]] (Nov. 2022)

==2021 Courses==
* [[Advgenemap2021|Advanced Gene Mapping]] (Online due to COVID)
* [[Genassoc2021|Genetic Association]] (Cancelled due to COVID19 restrictions)
* [[ComplexNGS2021|Complex Trait Analysis of Next Generation Sequence Data]]

==2020 Courses==
* [[Advgenemap2020|Advanced Gene Mapping]]
* [[Genassoc2020|Genetic Association]] (Cancelled due to COVID)
* [[ComplexNGS2020|Complex Trait Analysis of Next Generation Sequence Data]] (Cancelled due to COVID)

==2019 Courses==
* [[ComplexNGS2019|Complex Trait Analysis of Next Generation Sequence Data]]
* [[Genassoc2019|Genetic Association]]
* [[Advgenemap2019|Advanced Gene Mapping]]

==2018 Courses==
* [[Genassoc2018|Genetic Association]]
* [[ComplexNGS2018|NGS Analysis of Complex Traits]]
* [[Advgenemap2018|Advanced Gene Mapping]]

==2017 Courses==
* [[NGSMendelian2017|NGS Analysis of Mendelian Traits]]
* [[Genassoc2017|Genetic Association]]
* [[ComplexNGS2017|NGS Analysis of Complex Traits]]
* [[Advgenemap2017|Advanced Gene Mapping]]

==2016 Courses==
* [[NGSMendelian2016|NGS Analysis of Mendelian Traits - MDC Berlin]]
* [[Genassoc2016|Genetic Association -MDC Berlin]]
* [[ComplexNGS2016|NGS Analysis of Complex Traits- MDC Berlin]]
* [[Advgenemap2016|Advanced Gene Mapping - Rockefeller NYC]]

==2015 Courses==
* [[2015SeptMDC|NGS Analysis of Mendelian Traits - MDC Berlin]]
* [https://statgen.uni-koeln.de/courses/locations/germany/genetic-association-course-in-2015.php/Genetic Genetic Association- MDC Berlin]]
* [[2015MarchMDC|NGS Analysis of Complex Traits -MDC Berlin]]
* [[2015AdvancedGeneMapping|Advanced Gene Mapping - Rockefeller NYC]]

==2014 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/genetic-association-course-in-2014.php/ Genetic Association Course - MDC Berlin March 2014]
* [https://statgen.uni-koeln.de/courses/locations/germany/next-generation-sequence-data-analysis-course-in-2014.php/ Next Generation Sequence Data Analysis Course - MDC Berlin June 2014]

==2013 Course==
[https://statgen.uni-koeln.de/courses/locations/germany/genetic-association-course-in-2013.php/ Genetic Association Course - Berlin: June 2013]

==2012 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/genetic-association-course-in-2012.php/ Genetic Association Course - MDC Berlin July 2012]
* [https://statgen.uni-koeln.de/courses/locations/germany/gene-mapping-course-in-2012.php/ Gene Mapping Course - MDC Berlin November 2012]

==2011 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/genetic-association-course-in-2011.php/ Genetic Association Course - MDC Berlin July 2011]
* [https://statgen.uni-koeln.de/courses/locations/germany/gene-mapping-course-in-2011.php/ Gene Mapping Course -MDC Berlin November 2011]

==2010 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/genetic-association-course-in-2010.php/ Genetic Association Course - MDC Berlin May 2010]
* [https://statgen.uni-koeln.de/courses/locations/germany/gene-mapping-course-in-2010.php/ Gene Mapping Course - MDC Berlin October 2010]

==2009 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/gene-mapping-course-in-2009.php Gene Mapping Course - MDC Berlin: November 2009]

==2008 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/gene-mapping-course-in-2008.php/ Basic Gene Mapping Course - MDC Berlin: July 2008]

==2007 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/gene-mapping-course-in-2007.php/ Basic Gene Mapping Course - MDC Berlin: July 2007]

==2006 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/gene-mapping-course-in-2006.php/ Basic Gene Mapping Course - MDC Berlin: July 2006]

==2005 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/gene-mapping-course-in-2005.php/ Basic Gene Mapping Course - MDC Berlin July 2005]

==2004 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/gene-mapping-course-in-2004.php/ Basic Gene Mapping Course - MDC July 2004]

==2003 Course==
* [https://statgen.uni-koeln.de/courses/locations/germany/gene-mapping-course-in-2003.php Basic Gene Mapping Course - MDC Berlin: July 2003]

ComplexNGS2025

2025-06-16T20:24:03Z

Serveradmin: /* Complex Trait Analysis of Next Generation Sequence Data Course */

__NOTITLE__

=Complex Trait Analysis of Next Generation Sequence Data Course=
<div style="text-align: left;">September 8-12, 2025 
Max Delbrück Center (MDC) for Molecular Medicine 
Berlin, Germany</div>
----
The eighth Complex Trait Analysis of Next Generation Sequence Data Course will be held at the [https://www.mdc-berlin.de/ MDC] in Berlin from September 8 to 12, 2025. The course aims to teach the theory and application of methods for analyzing next-generation sequence (NGS) data for complex human traits. In addition to lectures, computer software will be used to analyze data, and problem-solving exercises will be performed to teach the trainees the latest method.

'''TOPICS:''' Sequence alignment, calling variants from NGS data, the VCF format, bioinformatic annotation of variants and regions, quality control of NGS data, association testing framework for quantitative and qualitative traits [fixed effects, random effects, linear mixed models (LMM) and generalized lMM (GLMM)], estimation of heritability, rare variant association methods, polygenic risk scores, pleiotropy, estimating power and sample size, and imputation of variants and their analysis

'''SOFTWARE''': ANNOVAR, BCFtools, GCTA, Genetic Power Calculator, FASTLMM, LDSC regression, LDPHRED2, R, REGENIE

'''INSTRUCTORS''': Suzanne Leal (Columbia University) and Michael Nothnagel (University of Cologne).

The cost of the 5-day course is €975 for researchers from an academic institution, and €1,950 for individuals from private (for-profit) companies. This fee covers tuition, A Monday evening welcome dinner, and course-related expenses (handouts, etc.) but not room, board, or additional meals. Housing is available for course participants at nearby hotels.

For additional information on the Complex Trait Analysis of NGS Data Course please contact [mailto:suzannemleal@gmail.com?subject=Complex%20Trait%20Analysis%20Course%20Berlin%202023 Suzanne Leal]:
Email: [mailto:suzannemleal@gmail.com?subject=Complex%20Trait%20Analysis%20Course%20Berlin%202023 suzannemleal@gmail.com]

'''

<div style="text-align: left;">[https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/schedules/schedule_berlin_complex_ngs_2025.pdf Click here for the course schedule]</div>
<div style="text-align: left;">[https://github.com/statgenetics/statgen-courses/raw/refs/heads/master/applications/Berlin_NGS_Complex_Trait_Application_2025.docx Click here for the application form]</div>
<div style="text-align: left;">[https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/flyer/Berlin_NGS_complex_traits_course_flyer_2025.pdf Click here for the course flyer (please post and distribute it)]</div>

MediaWiki:Sidebar

2025-04-14T19:59:45Z

Serveradmin:

* Short Courses
** Main_Page#Statistical_Genetics_Courses|Upcoming Courses
** Previous_Courses|Previous Courses

* Software
** http://gaow.github.io/genetic-analysis-software | Genetic Analysis Software
** Tutorials|Software Tutorials

* Course Materials
** Advgenemap2025|Advanced Gene Mapping (Jan. 2025)
*** https://github.com/statgenetics/statgen-courses/blob/master/release/AGMC_course_slides_2025.pdf | + Lecture Slides
*** https://github.com/statgenetics/statgen-courses/blob/master/release/AGMC_2025_exercise_booklet.pdf | + Exercises
** Advgenemap2024|Advanced Gene Mapping (April 2024)
*** https://statgen.us/files/2024/04/AGMC_lecture_booklet.pdf | + Lecture Slides
*** https://statgen.us/files/2024/04/AGMC_2024_excerise_booklet.pdf | + Exercises
** Advgenemap2023|Advanced Gene Mapping (May 2023)
*** https://statgen.us/files/2023/05/Lecture_booklet.pdf | + Lecture Slides
*** https://statgen.us/files/2023/05/Exercise_booklet_AGMC_May_23.pdf | + Exercises
** AdvgenemapNov2022|Advanced Gene Mapping (Nov. 2022)
*** https://statgen.us/files/2022/11/Exercise_booklet_AGMC_11_11_22.pdf | + Exercises
*** https://statgen.us/files/2022/11/Lectures_AGMC_November_2022.pdf | + Lectures
** Genassoc2022|Genetic Association (Sept. 2022)
*** https://statgen.us/files/2022/09/Exercise_booklet_9_26_22.pdf | + Exercises

MediaWiki:Sidebar

2025-04-14T19:59:19Z

Serveradmin:

* Short Courses
** Main_Page#Statistical_Genetics_Courses|Upcoming Courses
** Previous_Courses|Previous Courses

* Software
** http://gaow.github.io/genetic-analysis-software | Genetic Analysis Software
** Tutorials|Software Tutorials

* Course Materials

** Advgenemap2025|Advanced Gene Mapping (Jan. 2025)
*** https://github.com/statgenetics/statgen-courses/blob/master/release/AGMC_course_slides_2025.pdf | + Lecture Slides
*** https://github.com/statgenetics/statgen-courses/blob/master/release/AGMC_2025_exercise_booklet.pdf | + Exercises
** Advgenemap2024|Advanced Gene Mapping (April 2024)
*** https://statgen.us/files/2024/04/AGMC_lecture_booklet.pdf | + Lecture Slides
*** https://statgen.us/files/2024/04/AGMC_2024_excerise_booklet.pdf | + Exercises
** Advgenemap2023|Advanced Gene Mapping (May 2023)
*** https://statgen.us/files/2023/05/Lecture_booklet.pdf | + Lecture Slides
*** https://statgen.us/files/2023/05/Exercise_booklet_AGMC_May_23.pdf | + Exercises
** AdvgenemapNov2022|Advanced Gene Mapping (Nov. 2022)
*** https://statgen.us/files/2022/11/Exercise_booklet_AGMC_11_11_22.pdf | + Exercises
*** https://statgen.us/files/2022/11/Lectures_AGMC_November_2022.pdf | + Lectures
** Genassoc2022|Genetic Association (Sept. 2022)
*** https://statgen.us/files/2022/09/Exercise_booklet_9_26_22.pdf | + Exercises

MediaWiki:Sidebar

2025-04-14T19:58:49Z

Serveradmin:

* Short Courses
** Main_Page#Statistical_Genetics_Courses|Upcoming Courses
** Previous_Courses|Previous Courses

* Software
** http://gaow.github.io/genetic-analysis-software | Genetic Analysis Software
** Tutorials|Software Tutorials

* Course Materials

Advgenemap2025|Advanced Gene Mapping (Jan. 2025)

*** https://github.com/statgenetics/statgen-courses/blob/master/release/AGMC_course_slides_2025.pdf | + Lecture Slides
*** https://github.com/statgenetics/statgen-courses/blob/master/release/AGMC_2025_exercise_booklet.pdf | + Exercises
** Advgenemap2024|Advanced Gene Mapping (April 2024)
*** https://statgen.us/files/2024/04/AGMC_lecture_booklet.pdf | + Lecture Slides
*** https://statgen.us/files/2024/04/AGMC_2024_excerise_booklet.pdf | + Exercises
** Advgenemap2023|Advanced Gene Mapping (May 2023)
*** https://statgen.us/files/2023/05/Lecture_booklet.pdf | + Lecture Slides
*** https://statgen.us/files/2023/05/Exercise_booklet_AGMC_May_23.pdf | + Exercises
** AdvgenemapNov2022|Advanced Gene Mapping (Nov. 2022)
*** https://statgen.us/files/2022/11/Exercise_booklet_AGMC_11_11_22.pdf | + Exercises
*** https://statgen.us/files/2022/11/Lectures_AGMC_November_2022.pdf | + Lectures
** Genassoc2022|Genetic Association (Sept. 2022)
*** https://statgen.us/files/2022/09/Exercise_booklet_9_26_22.pdf | + Exercises

MediaWiki:Sidebar

2025-04-14T19:57:49Z

Serveradmin:

* Short Courses
** Main_Page#Statistical_Genetics_Courses|Upcoming Courses
** Previous_Courses|Previous Courses

* Software
** http://gaow.github.io/genetic-analysis-software | Genetic Analysis Software
** Tutorials|Software Tutorials

* Course Materials
** Advgenemap2025|Advanced Gene Mapping (Jan. 2025)
*** https://github.com/statgenetics/statgen-courses/blob/master/release/AGMC_course_slides_2025.pdf | • Lecture Slides
*** https://github.com/statgenetics/statgen-courses/blob/master/release/AGMC_2025_exercise_booklet.pdf | • Exercises
** Advgenemap2024|Advanced Gene Mapping (April 2024)
*** https://statgen.us/files/2024/04/AGMC_lecture_booklet.pdf | • Lecture Slides
*** https://statgen.us/files/2024/04/AGMC_2024_excerise_booklet.pdf | • Exercises
** Advgenemap2023|Advanced Gene Mapping (May 2023)
*** https://statgen.us/files/2023/05/Lecture_booklet.pdf | •- Lecture Slides
*** https://statgen.us/files/2023/05/Exercise_booklet_AGMC_May_23.pdf | • Exercises
** AdvgenemapNov2022|Advanced Gene Mapping (Nov. 2022)
*** https://statgen.us/files/2022/11/Exercise_booklet_AGMC_11_11_22.pdf | • Exercises
*** https://statgen.us/files/2022/11/Lectures_AGMC_November_2022.pdf | • Lectures
** Genassoc2022|Genetic Association (Sept. 2022)
*** https://statgen.us/files/2022/09/Exercise_booklet_9_26_22.pdf | • Exercises

MediaWiki:Sidebar

2025-04-14T19:55:40Z

Serveradmin:

* Short Courses
** Main_Page#Statistical_Genetics_Courses|Upcoming Courses
** Previous_Courses|Previous Courses

* Software
** http://gaow.github.io/genetic-analysis-software | Genetic Analysis Software
** Tutorials|Software Tutorials

* Course Materials
** Advgenemap2025|Advanced Gene Mapping (January 2025)
*** https://github.com/statgenetics/statgen-courses/blob/master/release/AGMC_course_slides_2025.pdf
*** https://github.com/statgenetics/statgen-courses/blob/master/release/AGMC_2025_exercise_booklet.pdf | - Lecture Slides | - Exercises
** Advgenemap2024|Advanced Gene Mapping (April 2024)
*** https://statgen.us/files/2024/04/AGMC_lecture_booklet.pdf | - Lecture Slides
*** https://statgen.us/files/2024/04/AGMC_2024_excerise_booklet.pdf | - Exercises
** Advgenemap2023|Advanced Gene Mapping (May 2023)
*** https://statgen.us/files/2023/05/Lecture_booklet.pdf | - Lecture Slides
*** https://statgen.us/files/2023/05/Exercise_booklet_AGMC_May_23.pdf | - Exercises
** AdvgenemapNov2022|Advanced Gene Mapping (Nov. 2022)
*** https://statgen.us/files/2022/11/Exercise_booklet_AGMC_11_11_22.pdf | - Exercises
*** https://statgen.us/files/2022/11/Lectures_AGMC_November_2022.pdf | - Lectures
** Genassoc2022|Genetic Association (Sept. 2022)
*** https://statgen.us/files/2022/09/Exercise_booklet_9_26_22.pdf | - Exercises

ComplexNGS2025

2025-02-10T21:44:32Z

Serveradmin:

__NOTITLE__

=Complex Trait Analysis of Next Generation Sequence Data Course=
<div style="text-align: left;">September 8-12, 2025 
Max Delbrück Center (MDC) for Molecular Medicine 
Berlin, Germany</div>
----
The eighth Complex Trait Analysis of Next Generation Sequence Data Course will be held at the [https://www.mdc-berlin.de/ MDC] in Berlin from September 8 to 12, 2025. The course aims to teach the theory and application of methods for analyzing next-generation sequence (NGS) data for complex human traits. In addition to lectures, computer software will be used to analyze data, and problem-solving exercises will be performed to teach the trainees the latest method.

'''TOPICS:''' Sequence alignment, calling variants from NGS data, the VCF format, bioinformatic annotation of variants and regions, quality control of NGS data, association testing framework for quantitative and qualitative traits [fixed effects, random effects, linear mixed models (LMM) and generalized lMM (GLMM)], estimation of heritability, rare variant association methods, polygenic risk scores, pleiotropy, estimating power and sample size, and imputation of variants and their analysis

'''SOFTWARE''': ANNOVAR, BCFtools, GCTA, Genetic Power Calculator, FASTLMM, LDSC regression, LDPHRED2, R, REGENIE

'''INSTRUCTORS''': Suzanne Leal (Columbia University) and Michael Nothnagel (University of Cologne).

The cost of the 5-day course is €975 for researchers from an academic institution, and €1,950 for individuals from private (for-profit) companies. This fee covers tuition, A Monday evening welcome dinner, and course-related expenses (handouts, etc.) but not room, board, or additional meals. Housing is available for course participants at nearby hotels.

For additional information on the Complex Trait Analysis of NGS Data Course please contact [mailto:suzannemleal@gmail.com?subject=Complex%20Trait%20Analysis%20Course%20Berlin%202023 Suzanne Leal]:
Email: [mailto:suzannemleal@gmail.com?subject=Complex%20Trait%20Analysis%20Course%20Berlin%202023 suzannemleal@gmail.com]

'''APPLICATION DEADLINE''': June 15, 2025

<div style="text-align: left;">[https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/schedules/schedule_berlin_complex_ngs_2025.pdf Click here for the course schedule]</div>
<div style="text-align: left;">[https://github.com/statgenetics/statgen-courses/raw/refs/heads/master/applications/Berlin_NGS_Complex_Trait_Application_2025.docx Click here for the application form]</div>
<div style="text-align: left;">[https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/flyer/Berlin_NGS_complex_traits_course_flyer_2025.pdf Click here for the course flyer (please post and distribute it)]</div>

ComplexNGS2025

2025-02-10T21:42:58Z

Serveradmin:

__NOTITLE__

=Complex Trait Analysis of Next Generation Sequence Data Course=
<div style="text-align: left;">September 8-12, 2025 
Max Delbrück Center (MDC) for Molecular Medicine 
Berlin, Germany</div>
----
The eighth Complex Trait Analysis of Next Generation Sequence Data Course will be held at the [https://www.mdc-berlin.de/ MDC] in Berlin from September 8 to 12, 2025. The course aims to teach the theory and application of methods for analyzing next-generation sequence (NGS) data for complex human traits. In addition to lectures, computer software will be used to analyze data, and problem-solving exercises will be performed to teach the trainees the latest method.

'''TOPICS:''' Sequence alignment, calling variants from NGS data, the VCF format, bioinformatic annotation of variants and regions, quality control of NGS data, association testing framework for quantitative and qualitative traits [fixed effects, random effects, linear mixed models (LMM) and generalized lMM (GLMM)], estimation of heritability, rare variant association methods, polygenic risk scores, pleiotropy, estimating power and sample size, and imputation of variants and their analysis

'''SOFTWARE''': ANNOVAR, BCFtools, GCTA, Genetic Power Calculator, FASTLMM, LDSC regression, LDPHRED2, R, REGENIE

'''INSTRUCTORS''': Suzanne Leal (Columbia University) and Michael Nothnagel (University of Cologne).

The cost of the 5-day course is €975 for researchers from an academic institution, and €1,950 for individuals from private (for-profit) companies. This fee covers tuition, A Monday evening welcome dinner, and course-related expenses (handouts, etc.) but not room, board, or additional meals. Housing is available for course participants at nearby hotels.

For additional information on the Complex Trait Analysis of NGS Data Course please contact [mailto:suzannemleal@gmail.com?subject=Complex%20Trait%20Analysis%20Course%20Berlin%202023 Suzanne Leal]:
Email: [mailto:suzannemleal@gmail.com?subject=Complex%20Trait%20Analysis%20Course%20Berlin%202023 suzannemleal@gmail.com]

'''APPLICATION DEADLINE''': June 15, 2025

<div style="text-align: left;">[https://github.com/statgenetics/statgen-courses/blob/master/schedules/schedule_berlin_complex_ngs_2025.pdf Click here for the course schedule]</div>
<div style="text-align: left;">[https://github.com/statgenetics/statgen-courses/raw/refs/heads/master/applications/Berlin_NGS_Complex_Trait_Application_2025.docx Click here for the application form]</div>
<div style="text-align: left;">[https://raw.githubusercontent.com/statgenetics/statgen-courses/refs/heads/master/flyer/Berlin_NGS_complex_traits_course_flyer_2025.pdf Click here for the course flyer (please post and distribute it)]</div>

ComplexNGS2025

2025-02-10T21:39:52Z

Serveradmin:

__NOTITLE__

=Complex Trait Analysis of Next Generation Sequence Data Course=
<div style="text-align: left;">September 8-12, 2025 
Max Delbrück Center (MDC) for Molecular Medicine 
Berlin, Germany</div>
----
The eighth Complex Trait Analysis of Next Generation Sequence Data Course will be held at the [https://www.mdc-berlin.de/ MDC] in Berlin from September 8 to 12, 2025. The course aims to teach the theory and application of methods for analyzing next-generation sequence (NGS) data for complex human traits. In addition to lectures, computer software will be used to analyze data, and problem-solving exercises will be performed to teach the trainees the latest method.

'''TOPICS:''' Sequence alignment, calling variants from NGS data, the VCF format, bioinformatic annotation of variants and regions, quality control of NGS data, association testing framework for quantitative and qualitative traits [fixed effects, random effects, linear mixed models (LMM) and generalized lMM (GLMM)], estimation of heritability, rare variant association methods, polygenic risk scores, pleiotropy, estimating power and sample size, and imputation of variants and their analysis

'''SOFTWARE''': ANNOVAR, BCFtools, GCTA, Genetic Power Calculator, FASTLMM, LDSC regression, LDPHRED2, R, REGENIE

'''INSTRUCTORS''': Suzanne Leal (Columbia University) and Michael Nothnagel (University of Cologne).

The cost of the 5-day course is €975 for researchers from an academic institution, and €1,950 for individuals from private (for-profit) companies. This fee covers tuition, A Monday evening welcome dinner, and course-related expenses (handouts, etc.) but not room, board, or additional meals. Housing is available for course participants at nearby hotels.

For additional information on the Complex Trait Analysis of NGS Data Course please contact [mailto:suzannemleal@gmail.com?subject=Complex%20Trait%20Analysis%20Course%20Berlin%202023 Suzanne Leal]:
Email: [mailto:suzannemleal@gmail.com?subject=Complex%20Trait%20Analysis%20Course%20Berlin%202023 suzannemleal@gmail.com]

'''APPLICATION DEADLINE''': June 15, 2025

<div style="text-align: left;">[https://github.com/statgenetics/statgen-courses/blob/master/schedules/schedule_berlin_complex_ngs_2025.pdf Click here for the course schedule]</div>
<div style="text-align: left;">[https://github.com/statgenetics/statgen-courses/raw/refs/heads/master/applications/Berlin_NGS_Complex_Trait_Application_2025.docx Click here for the application form]</div>
<div style="text-align: left;">[https://github.com/statgenetics/statgen-courses/blob/master/flyer/Berlin_NGS_complex_traits_course_flyer_2025.pdf Click here for the course flyer (please post and distribute it)]</div>

ComplexNGS2025

2025-02-10T21:39:18Z

Serveradmin: /* Complex Trait Analysis of Next Generation Sequence Data Course */

__NOTITLE__

<div style="text-align: center;">
=Complex Trait Analysis of Next Generation Sequence Data Course=
<div style="text-align: left;">September 8-12, 2025 
Max Delbrück Center (MDC) for Molecular Medicine 
Berlin, Germany</div>
----
The eighth Complex Trait Analysis of Next Generation Sequence Data Course will be held at the [https://www.mdc-berlin.de/ MDC] in Berlin from September 8 to 12, 2025. The course aims to teach the theory and application of methods for analyzing next-generation sequence (NGS) data for complex human traits. In addition to lectures, computer software will be used to analyze data, and problem-solving exercises will be performed to teach the trainees the latest method.

'''TOPICS:''' Sequence alignment, calling variants from NGS data, the VCF format, bioinformatic annotation of variants and regions, quality control of NGS data, association testing framework for quantitative and qualitative traits [fixed effects, random effects, linear mixed models (LMM) and generalized lMM (GLMM)], estimation of heritability, rare variant association methods, polygenic risk scores, pleiotropy, estimating power and sample size, and imputation of variants and their analysis

'''SOFTWARE''': ANNOVAR, BCFtools, GCTA, Genetic Power Calculator, FASTLMM, LDSC regression, LDPHRED2, R, REGENIE

'''INSTRUCTORS''': Suzanne Leal (Columbia University) and Michael Nothnagel (University of Cologne).

The cost of the 5-day course is €975 for researchers from an academic institution, and €1,950 for individuals from private (for-profit) companies. This fee covers tuition, A Monday evening welcome dinner, and course-related expenses (handouts, etc.) but not room, board, or additional meals. Housing is available for course participants at nearby hotels.

For additional information on the Complex Trait Analysis of NGS Data Course please contact [mailto:suzannemleal@gmail.com?subject=Complex%20Trait%20Analysis%20Course%20Berlin%202023 Suzanne Leal]:
Email: [mailto:suzannemleal@gmail.com?subject=Complex%20Trait%20Analysis%20Course%20Berlin%202023 suzannemleal@gmail.com]

'''APPLICATION DEADLINE''': June 15, 2025

<div style="text-align: left;">[https://github.com/statgenetics/statgen-courses/blob/master/schedules/schedule_berlin_complex_ngs_2025.pdf Click here for the course schedule]</div>
<div style="text-align: left;">[https://github.com/statgenetics/statgen-courses/raw/refs/heads/master/applications/Berlin_NGS_Complex_Trait_Application_2025.docx Click here for the application form]</div>
<div style="text-align: left;">[https://github.com/statgenetics/statgen-courses/blob/master/flyer/Berlin_NGS_complex_traits_course_flyer_2025.pdf Click here for the course flyer (please post and distribute it)]</div>

ComplexNGS2025

2025-02-10T21:23:36Z

Serveradmin: /* Complex Trait Analysis of Next Generation Sequence Data Course */

__NOTITLE__

<div style="text-align: center;">
=Complex Trait Analysis of Next Generation Sequence Data Course=
<div style="text-align: left;">September 8-12, 2025 
Max Delbrück Center (MDC) for Molecular Medicine 
Berlin, Germany</div>
----
The eighth Complex Trait Analysis of Next Generation Sequence Data Course will be held at the [https://www.mdc-berlin.de/ MDC] in Berlin from September 8 to 12, 2025. The course aims to teach the theory and application of methods for analyzing next-generation sequence (NGS) data for complex human traits. In addition to lectures, computer software will be used to analyze data, and problem-solving exercises will be performed to teach the trainees the latest method.

TOPICS: Sequence alignment, calling variants from NGS data, the VCF format, bioinformatic annotation of variants and regions, quality control of NGS data, association testing framework for quantitative and qualitative traits [fixed effects, random effects, linear mixed models (LMM) and generalized lMM (GLMM)], estimation of heritability, rare variant association methods, polygenic risk scores, pleiotropy, estimating power and sample size, and imputation of variants and their analysis

SOFTWARE: ANNOVAR, BCFtools, GCTA, Genetic Power Calculator, FASTLMM, LDSC regression, LDPHRED2, R, REGENIE

INSTRUCTORS: Suzanne Leal (Columbia University) and Michael Nothnagel (University of Cologne).

The cost of the 5-day course is €975 for researchers from an academic institution, and €1,950 for individuals from private (for-profit) companies. This fee covers tuition, A Monday evening welcome dinner, and course-related expenses (handouts, etc.) but not room, board, or additional meals. Housing is available for course participants at nearby hotels.

For additional information on the Complex Trait Analysis of NGS Data Course please contact [mailto:suzannemleal@gmail.com?subject=Complex%20Trait%20Analysis%20Course%20Berlin%202023 Suzanne Leal]:
Email: [mailto:suzannemleal@gmail.com?subject=Complex%20Trait%20Analysis%20Course%20Berlin%202023 suzannemleal@gmail.com]

APPLICATION DEADLINE: June 15, 2025

<div style="text-align: left;">[https://github.com/statgenetics/statgen-courses/blob/master/schedules/schedule_berlin_complex_ngs_2025.pdf Click here for the course schedule]</div>
<div style="text-align: left;">[https://github.com/statgenetics/statgen-courses/raw/refs/heads/master/applications/Berlin_NGS_Complex_Trait_Application_2025.docx Click here for the application form]</div>
<div style="text-align: left;">[https://github.com/statgenetics/statgen-courses/blob/master/flyer/Berlin_NGS_complex_traits_course_flyer_2025.pdf Click here for the course flyer (please post and distribute it)]</div>

ComplexNGS2025

2025-02-10T21:22:45Z

Serveradmin: /* Complex Trait Analysis of Next Generation Sequence Data Course */

__NOTITLE__

<div style="text-align: center;">
=Complex Trait Analysis of Next Generation Sequence Data Course=
<div style="text-align: left;">September 8-12, 2025 
Max Delbrück Center (MDC) for Molecular Medicine 
Berlin, Germany</div>
----
The eighth Complex Trait Analysis of Next Generation Sequence Data Course will be held at the [https://www.mdc-berlin.de/ MDC] in Berlin from September 8 to 12, 2025. The course aims to teach the theory and application of methods for analyzing next-generation sequence (NGS) data for complex human traits. In addition to lectures, computer software will be used to analyze data, and problem-solving exercises will be performed to teach the trainees the latest method.

<div style="text-align: left;">TOPICS: Sequence alignment, calling variants from NGS data, the VCF format, bioinformatic annotation of variants and regions, quality control of NGS data, association testing framework for quantitative and qualitative traits [fixed effects, random effects, linear mixed models (LMM) and generalized lMM (GLMM)], estimation of heritability, rare variant association methods, polygenic risk scores, pleiotropy, estimating power and sample size, and imputation of variants and their analysis</div>
SOFTWARE: ANNOVAR, BCFtools, GCTA, Genetic Power Calculator, FASTLMM, LDSC regression, LDPHRED2, R, REGENIE

INSTRUCTORS: Suzanne Leal (Columbia University) and Michael Nothnagel (University of Cologne).

The cost of the 5-day course is €975 for researchers from an academic institution, and €1,950 for individuals from private (for-profit) companies. This fee covers tuition, A Monday evening welcome dinner, and course-related expenses (handouts, etc.) but not room, board, or additional meals. Housing is available for course participants at nearby hotels.

For additional information on the Complex Trait Analysis of NGS Data Course please contact [mailto:suzannemleal@gmail.com?subject=Complex%20Trait%20Analysis%20Course%20Berlin%202023 Suzanne Leal]:
Email: [mailto:suzannemleal@gmail.com?subject=Complex%20Trait%20Analysis%20Course%20Berlin%202023 suzannemleal@gmail.com]

APPLICATION DEADLINE: June 15, 2025

<div style="text-align: left;">[https://github.com/statgenetics/statgen-courses/blob/master/schedules/schedule_berlin_complex_ngs_2025.pdf Click here for the course schedule]</div>
<div style="text-align: left;">[https://github.com/statgenetics/statgen-courses/raw/refs/heads/master/applications/Berlin_NGS_Complex_Trait_Application_2025.docx Click here for the application form]</div>
<div style="text-align: left;">[https://github.com/statgenetics/statgen-courses/blob/master/flyer/Berlin_NGS_complex_traits_course_flyer_2025.pdf Click here for the course flyer (please post and distribute it)]</div>

ComplexNGS2025

2025-02-10T21:21:54Z

Serveradmin: /* Complex Trait Analysis of Next Generation Sequence Data Course */

__NOTITLE__

<div style="text-align: center;">
=Complex Trait Analysis of Next Generation Sequence Data Course=
<div style='text-align: left;'>September 8-12, 2025 
Max Delbrück Center (MDC) for Molecular Medicine 
Berlin, Germany</div>
----

<div style='text-align: left;'>The eighth Complex Trait Analysis of Next Generation Sequence Data Course will be held at the [https://www.mdc-berlin.de/ MDC] in Berlin from September 8 to 12, 2025. The course aims to teach the theory and application of methods for analyzing next-generation sequence (NGS) data for complex human traits. In addition to lectures, computer software will be used to analyze data, and problem-solving exercises will be performed to teach the trainees the latest method.</div>

<div style='text-align: left;'>TOPICS: Sequence alignment, calling variants from NGS data, the VCF format, bioinformatic annotation of variants and regions, quality control of NGS data, association testing framework for quantitative and qualitative traits [fixed effects, random effects, linear mixed models (LMM) and generalized lMM (GLMM)], estimation of heritability, rare variant association methods, polygenic risk scores, pleiotropy, estimating power and sample size, and imputation of variants and their analysis</div>

<div style='text-align: left;'>SOFTWARE: ANNOVAR, BCFtools, GCTA, Genetic Power Calculator, FASTLMM, LDSC regression, LDPHRED2, R, REGENIE</div>

<div style='text-align: left;'>INSTRUCTORS: Suzanne Leal (Columbia University) and Michael Nothnagel (University of Cologne).</div>

<div style='text-align: left;'>The cost of the 5-day course is €975 for researchers from an academic institution, and €1,950 for individuals from private (for-profit) companies. This fee covers tuition, A Monday evening welcome dinner, and course-related expenses (handouts, etc.) but not room, board, or additional meals. Housing is available for course participants at nearby hotels.</div>

<div style='text-align: left;'>For additional information on the Complex Trait Analysis of NGS Data Course please contact [mailto:suzannemleal@gmail.com?subject=Complex%20Trait%20Analysis%20Course%20Berlin%202023 Suzanne Leal]:
Email: [mailto:suzannemleal@gmail.com?subject=Complex%20Trait%20Analysis%20Course%20Berlin%202023 suzannemleal@gmail.com]</div>

<div style='text-align: left;'>APPLICATION DEADLINE: June 15, 2025</div>

<div style='text-align: left;'>[https://github.com/statgenetics/statgen-courses/blob/master/schedules/schedule_berlin_complex_ngs_2025.pdf Click here for the course schedule]</div>

<div style='text-align: left;'>[https://github.com/statgenetics/statgen-courses/raw/refs/heads/master/applications/Berlin_NGS_Complex_Trait_Application_2025.docx Click here for the application form]</div>

<div style='text-align: left;'>[https://github.com/statgenetics/statgen-courses/blob/master/flyer/Berlin_NGS_complex_traits_course_flyer_2025.pdf Click here for the course flyer (please post and distribute it)]</div>

ComplexNGS2025

2025-02-10T21:21:06Z

Serveradmin: /* Complex Trait Analysis of Next Generation Sequence Data Course */

ComplexNGS2025

2025-02-10T21:20:28Z

Serveradmin: /* Complex Trait Analysis of Next Generation Sequence Data Course */

__NOTITLE__

<div style="text-align: center;">
=Complex Trait Analysis of Next Generation Sequence Data Course=
September 8-12, 2025 
Max Delbrück Center (MDC) for Molecular Medicine 
Berlin, Germany

----

The eighth Complex Trait Analysis of Next Generation Sequence Data Course will be held at the [https://www.mdc-berlin.de/ MDC] in Berlin from September 8 to 12, 2025. The course aims to teach the theory and application of methods for analyzing next-generation sequence (NGS) data for complex human traits. In addition to lectures, computer software will be used to analyze data, and problem-solving exercises will be performed to teach the trainees the latest method.

TOPICS: Sequence alignment, calling variants from NGS data, the VCF format, bioinformatic annotation of variants and regions, quality control of NGS data, association testing framework for quantitative and qualitative traits [fixed effects, random effects, linear mixed models (LMM) and generalized lMM (GLMM)], estimation of heritability, rare variant association methods, polygenic risk scores, pleiotropy, estimating power and sample size, and imputation of variants and their analysis

SOFTWARE: ANNOVAR, BCFtools, GCTA, Genetic Power Calculator, FASTLMM, LDSC regression, LDPHRED2, R, REGENIE

INSTRUCTORS: Suzanne Leal (Columbia University) and Michael Nothnagel (University of Cologne).

The cost of the 5-day course is €975 for researchers from an academic institution, and €1,950 for individuals from private (for-profit) companies. This fee covers tuition, A Monday evening welcome dinner, and course-related expenses (handouts, etc.) but not room, board, or additional meals. Housing is available for course participants at nearby hotels.

For additional information on the Complex Trait Analysis of NGS Data Course please contact [mailto:suzannemleal@gmail.com?subject=Complex%20Trait%20Analysis%20Course%20Berlin%202023 Suzanne Leal]:
Email: [mailto:suzannemleal@gmail.com?subject=Complex%20Trait%20Analysis%20Course%20Berlin%202023 suzannemleal@gmail.com]

APPLICATION DEADLINE: June 15, 2025

[https://github.com/statgenetics/statgen-courses/blob/master/schedules/schedule_berlin_complex_ngs_2025.pdf Click here for the course schedule]

[https://github.com/statgenetics/statgen-courses/raw/refs/heads/master/applications/Berlin_NGS_Complex_Trait_Application_2025.docx Click here for the application form]

[https://github.com/statgenetics/statgen-courses/blob/master/flyer/Berlin_NGS_complex_traits_course_flyer_2025.pdf Click here for the course flyer (please post and distribute it)]

ComplexNGS2025

2025-02-10T21:18:23Z

Serveradmin: /* Complex Trait Analysis of Next Generation Sequence Data Course */

__NOTITLE__

<div style="text-align: center;">
=Complex Trait Analysis of Next Generation Sequence Data Course=
September 8-12, 2025 
Max Delbrück Center (MDC) for Molecular Medicine 
Berlin, Germany

----

The eighth Berlin Complex Trait Analysis of Next Generation Sequence Data Course will be held at the [https://www.mdc-berlin.de/ MDC] in Berlin from September 8 to 12, 2025. The course aims to teach the theory and application of methods for analyzing next-generation sequence (NGS) data for complex human traits. In addition to lectures, computer software will be used to analyze data, and problem-solving exercises will be performed to teach the trainees the latest method.

TOPICS: Sequence alignment, calling variants from NGS data, the VCF format, bioinformatic annotation of variants and regions, quality control of NGS data, association testing framework for quantitative and qualitative traits [fixed effects, random effects, linear mixed models (LMM) and generalized lMM (GLMM)], estimation of heritability, rare variant association methods, polygenic risk scores, pleiotropy, estimating power and sample size, and imputation of variants and their analysis

SOFTWARE: ANNOVAR, BCFtools, GCTA, Genetic Power Calculator, FASTLMM, LDSC regression, LDPHRED2, R, REGENIE

INSTRUCTORS: Suzanne Leal (Columbia University) and Michael Nothnagel (University of Cologne).

The cost of the 5-day course is €975 for researchers from an academic institution, and €1,950 for individuals from private (for-profit) companies. This fee covers tuition, A Monday evening welcome dinner, and course-related expenses (handouts, etc.) but not room, board, or additional meals. Housing is available for course participants at nearby hotels.

For additional information on the Complex Trait Analysis of NGS Data Course please contact [mailto:suzannemleal@gmail.com?subject=Complex%20Trait%20Analysis%20Course%20Berlin%202023 Suzanne Leal]:
Email: [mailto:suzannemleal@gmail.com?subject=Complex%20Trait%20Analysis%20Course%20Berlin%202023 suzannemleal@gmail.com]

APPLICATION DEADLINE: June 15, 2025

[https://github.com/statgenetics/statgen-courses/blob/master/schedules/schedule_berlin_complex_ngs_2025.pdf Click here for the course schedule]

[https://github.com/statgenetics/statgen-courses/raw/refs/heads/master/applications/Berlin_NGS_Complex_Trait_Application_2025.docx Click here for the application form]

[https://github.com/statgenetics/statgen-courses/blob/master/flyer/Berlin_NGS_complex_traits_course_flyer_2025.pdf Click here for the course flyer (please post and distribute it)]