2015JuneMDC - Revision history

Serveradmin: /* Data Sets Used During the Course */

2016-06-07T17:09:58Z

‎Data Sets Used During the Course

Serveradmin: /* Course Slides */

2016-06-07T17:09:47Z

‎Course Slides

Serveradmin: /* Course Instructors */

2016-05-05T20:21:26Z

‎Course Instructors

Serveradmin at 20:20, 5 May 2016

2016-05-05T20:20:28Z

Serveradmin at 17:58, 5 May 2016

2016-05-05T17:58:37Z

Serveradmin: Created page with " NOTITLE Genetic Association Course with Application to Sequence and Genotype Data June 22-26, 2015, Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany G..."

2016-05-05T17:58:23Z

Created page with "__ NOTITLE __ Genetic Association Course with Application to Sequence and Genotype Data June 22-26, 2015, Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany G..."

New page

__ NOTITLE __
Genetic Association Course with Application to Sequence and Genotype Data

June 22-26, 2015, Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany
General Information
The goal of the course is to teach the course participants both theory and application of methods for population based association analysis, with a concentration on the analysis of exome and whole genome sequence and genotype data.
Emphasis in this course is on strategies for genetic mapping of complex human traits. It will include theory as well as practical exercises. The exercises will be carried out using a variety of computer programs (PLINK, GenABEL, MACH, UNPHASED, EIGENSTRAT, Variant Association Tools (VAT), SEQPower and R, etc.) and with pencil and paper. The emphasis of this course is analysis of population based whole genome and exome data including genotype and sequence data. TOPICS include: Association analysis of qualitative and quantitative traits; single marker and haplotype analysis; analysis of whole genome association study data; complex trait rare variant association analysis of next generation sequence data; data quality control for genotype and next generation sequence data; haplotype reconstruction; tagSNPselection; controlling population admixture (genomic control, principal components analysis, etc); imputing genotype data from sequence and genotype data; detecting gene x gene and gene x environmental interactions; power and sample size estimation for both genotype and rare variant data; permutation (estimating empirical p-values); and false discovery rate (FDR).
Link to Berlin hotel tax exemption form
Direction to the MDC Campus
0Direction to the classroom
Location:
MDC - communication center (Building C83 on the Campus Map)
Room Axion 2 ¶ The building is red and stands across the street from the campus bus stop and the blue bear. ¶
Course Instructors
The organizers and instructors for the course are Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne).

Commands for Computer Exercises
View here
Course Slides
Download here
Data Sets Used During the Course
Download here
Software Links
EIGENSTRAT
GenABEL
PLINK
R
SEQPower
UNPHASED
Variant Association Tools

@@ Line 34: / Line 34: @@
 ===Data Sets Used During the Course===
-::* [http://statgen.us/files/2016/06/june2015berlin.tar.bz2 Download here]
+::* [http://statgen.us/files/2015/06/june2015berlin.tar.bz2 Download here]
 ===Software Links===

@@ Line 31: / Line 31: @@
 ===Course Slides===
-::* [http://statgen.us/uploads/berlin_course_June_2015.pdf Download here]
+::* [http://statgen.us/files/2015/06/berlin_course_June_2015.pdf Download here]
 ===Data Sets Used During the Course===

@@ Line 21: / Line 21: @@
 The organizers and instructors for the course are Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne).
-<img src="https://statgen.research.bcm.edu/files/img/2015JuneInstructors.jpg" width=226" height="301">
+<img src="https://statgen.research.bcm.edu/files/img/2015JuneInstructors.jpg" width="226" height="301">
 <!--[[File:2015JuneInstructors.jpg|none|226x301px]]-->
-[[File:2015JuneMDC_Class.jpeg|none|500x373px]]
+<img src="https://statgen.research.bcm.edu/files/img/2015JuneMDC_Class.jpg" width="500" height="373">
 ===Commands for Computer Exercises===

@@ Line 21: / Line 21: @@
 The organizers and instructors for the course are Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne).
-[[File:2015JuneInstructors.jpg|none|226x301px]]
+<img src="https://statgen.research.bcm.edu/files/img/2015JuneInstructors.jpg" width=226" height="301">
 [[File:2015JuneMDC_Class.jpeg|none|500x373px]]

@@ Line 1: / Line 1: @@
-__ NOTITLE __
+__NOTITLE__
-Genetic Association Course with Application to Sequence and Genotype Data
 June 22-26, 2015, Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany
 General Information
 The goal of the course is to teach the course participants both theory and application of methods for population based association analysis, with a concentration on the analysis of exome and whole genome sequence and genotype data.
-Emphasis in this course is on strategies for genetic mapping of complex human traits. It will include theory as well as practical exercises. The exercises will be carried out using a variety of computer programs (PLINK, GenABEL, MACH, UNPHASED, EIGENSTRAT, Variant Association Tools (VAT), SEQPower and R, etc.) and with pencil and paper. The emphasis of this course is analysis of population based whole genome and exome data including genotype and sequence data.  TOPICS include: Association analysis of qualitative and quantitative traits; single marker and haplotype analysis; analysis of whole genome association study data; complex trait rare variant association analysis of next generation sequence data; data quality control for genotype and next generation sequence data; haplotype reconstruction; tagSNPselection; controlling population admixture (genomic  control, principal components analysis, etc); imputing genotype data from sequence and genotype data; detecting gene x gene and gene x environmental interactions; power and sample size estimation for both genotype and rare variant data; permutation (estimating empirical p-values); and false discovery rate (FDR).
-Link to Berlin hotel tax exemption form
+Emphasis in this course is on strategies for genetic mapping of complex human traits. It will include theory as well as practical exercises. The exercises will be carried out using a variety of computer programs (PLINK,&nbsp;GenABEL, MACH, UNPHASED, EIGENSTRAT, Variant Association Tools (VAT),&nbsp;SEQPower&nbsp;and R, etc.) and with pencil and paper. The emphasis of this course is analysis of population based whole genome and exome data including genotype and sequence data.&nbsp;&nbsp;TOPICS include: Association analysis of qualitative and quantitative traits; single marker and haplotype analysis; analysis of whole genome association study data; complex trait rare variant association analysis of next generation sequence data; data quality control for genotype and next generation sequence data;&nbsp;haplotype&nbsp;reconstruction;&nbsp;tagSNPselection; controlling population admixture (genomic&nbsp;&nbsp;control, principal components analysis, etc); imputing genotype data from sequence and genotype data; detecting gene x gene and gene x environmental interactions; power and sample size estimation for both genotype and rare variant data; permutation (estimating empirical p-values); and false discovery rate (FDR).
 Direction to the MDC Campus
-Direction to the classroom
+=====[[Media:BerlinHotelExemption.pdf|Link to Berlin hotel tax exemption form]]=====
 Location:
 MDC - communication center (Building C83 on the Campus Map)
-Room Axion 2  ¶ The building is red and stands across the street from the campus bus stop and the blue bear. ¶
+:: MDC - communication center (Building C83 on the [http://www.campus-berlin-buch.de/en/location/ Campus Map])
-Course Instructors
+:: Room Axion 2&nbsp;
 The organizers and instructors for the course are Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne).
-Commands for Computer Exercises
+===Software Links===
-View here
+::* EIGENSTRAT
-Course Slides
+::* [http://www.genabel.org/ GenABEL]
-Download here
+::* [http://pngu.mgh.harvard.edu/~purcell/plink/ PLINK]
-Data Sets Used During the Course
+::* [http://www.r-project.org/ R]
-Download here
+::* [http://www.bioinformatics.org/spower/start SEQPower]
-Software Links
+::* [https://sites.google.com/site/fdudbridge/software/unphased-3-1 UNPHASED]
-EIGENSTRAT
+::* [http://varianttools.sf.net/VAT Variant Association Tools]
 GenABEL
 PLINK
-−
 SEQPower
 UNPHASED
 Variant Association Tools