Difference between revisions of "NGSMendelian2017"
From Statistical Genetics Courses
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::* Alohomora ([http://gmc.mdc-berlin.de/alohomora/previous_releases/alohomora_v0.32_linux.zip Linux] [http://gmc.mdc-berlin.de/alohomora/previous_releases/alohomora_v0.32-win32.zip Windows]) | ::* Alohomora ([http://gmc.mdc-berlin.de/alohomora/previous_releases/alohomora_v0.32_linux.zip Linux] [http://gmc.mdc-berlin.de/alohomora/previous_releases/alohomora_v0.32-win32.zip Windows]) | ||
::** [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Data Set] | ::** [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Data Set] | ||
| − | + | IGV ([https://statgen.research.bcm.edu/files/software/igv/igv-2.3.97.jar igv.jar]) | |
::** [https://statgen.research.bcm.edu/files/2017/09/data/igv_exercise.zip BAM and VCF Files] | ::** [https://statgen.research.bcm.edu/files/2017/09/data/igv_exercise.zip BAM and VCF Files] | ||
| + | X11 support | ||
| + | ::** [https://sourceforge.net/projects/xming/ Xming (for Windows)] | ||
| + | ::** [https://www.xquartz.org/index.html XQuartz (for macOS)] | ||
===Commands for Computer Exercises=== | ===Commands for Computer Exercises=== | ||
Revision as of 17:04, 14 September 2017
Contents
- 1 Identifying Genes for Mendelian Traits using Next Generation Sequence Data
Identifying Genes for Mendelian Traits using Next Generation Sequence Data
September 18-22, 2017
Max Delbrück Center (MDC) for Molecular Medicine
Berlin, Germany
The Identifying Genes for Mendelian Traits using Next Generation Sequence Data Course will be held at the MDC in Berlin from September 18-22, 2017. The goal of the course is to teach the course participants both theory and application of methods to identify genes for Mendelian diseases/traits using filtering methods, homozygosity mapping and linkage analysis.
Emphasis in this course is on strategies for gene mapping and variant/gene identification for Mendelian Traits. It will include theory as well as practical exercises. The exercises will be carried out using a variety of computer programs (e.g. Gemini, GeneHunter, GERP, Homozygosity Mapper, Integrative Genome Viewer, MERLIN, PhlyoP, Polyphen, SEQLinkage, Variant Mendelian Tools,) and with pencil and paper. TOPICS include: study design; linkage analysis and homozygosity mapping using genotype array and next generation sequence data (exome and whole genome), haplotype reconstruction, evaluating pedigree informativeness and power to detect linkage, vcf file annotation; generation of NGS data; identification of causal variants using filter approaches, variant annotation, evaluation of deleterious effects of variants and their functionality. The organizers and instructors for the course are Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne).
The cost of the 5 day course is 975 EUR for researchers from an academic institution, and 1,950 EUR for individuals from private (for profit) companies. This fee covers tuition, Monday evening wine and cheese party and course related expenses (handouts, etc.) but not room, board or meals. Inexpensive housing is available for course participants at the MDC and nearby hotels. The maximum number of participants is 40.
For additional information on the course please contact Suzanne Leal:
- email: sleal@bcm.edu
- Tel: +1 (713) 798-4011
- Fax: +1 (713) 798-4012
Link to Berlin hotel tax exemption form
Direction to the MDC Campus
Direction 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).
Downloads for Course
IGV (igv.jar)
X11 support
Commands for Computer Exercises
Data Sets
Software Links
Databases
Bioinformatic Tools
Other Links
Click here for course schedule
Click here for the application form
Click here for course flyer (please post and distribute)
Click here for maps and directions to the MDC
Click here for the information on MDC Housing
Click here for Berlin tourist information
Click here and like us on Facebook
Click here for photos and data from Genetic Association Course – Berlin: September 2016
Click here for photos and datasets from Analysis of Next Generation Sequence Data for Complex Traits Course – Berlin: July 2016
Click here for photos and datasets from the Analysis of Next Generation Sequence Data Mendelian Traits - Berlin: September 2015
Click here for photos and datasets from the Genetic Association Course - Berlin: June 2015
Click here for photos and datasets from the Analysis of Next Generation Sequence Data Complex Traits - Berlin: March 2015
Click here for photos and datasets from the Genetic Association Course - Berlin: June 2015
Click here for photos and datasets from the Complex Trait Analysis of NGS Data Course - Berlin: March 2015
Click here for photos and datasets from the Next Generation Sequence Data Analysis Course - Berlin: June 2014
Click here for photos and datasets from the Genetic Association Course - Berlin: March 2014
Click here for photos and datasets from the Genetic Association Course - Berlin: June 2013
Click here for photos and datasets from the Basic Gene Mapping Course - Berlin: November 2012
Click here for photos from the Genetic Association Course - Berlin: July 2012
Click here for photos from the Basic Gene Mapping Course - Berlin: November 2011
Click here for photos from the Genetic Association Course - Berlin: July 2011
Click here for photos from the Basic Gene Mapping Course - Berlin: October 2010
Click here for photos from the Genetic Association Course - Berlin: May 2010
Click here for photos from the Basic Gene Mapping Course - Berlin: November 2009
Click here for photos from the Basic Gene Mapping Course - Berlin: July 2008
Click here for photos from the Basic Gene Mapping Course - Berlin: July 2007
Click here for photos from the Basic Gene Mapping Course - Berlin: July 2006
Click here for photos from the Basic Gene Mapping Course - Berlin: July 2005
Click here for photos from the Basic Gene Mapping Course - Berlin: July 2004
Click here for photos from the Basic Gene Mapping Course - Berlin: July 2003
