Difference between revisions of "NGSMendelian2016"
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| − | =====[https://statgen.research.bcm.edu/files/2016/10/Schedule_NGS_Mendelian_2016.pdf Click here for course schedule]===== | + | =====[https://statgen.research.bcm.edu/files/2016/10/Schedule_NGS_Mendelian_2016.pdf Click here for course schedule]===== |
| − | + | =====[http://statgen.us/files/2016/10/BerlinHotelTaxExemptionForm.pdf Link to Berlin hotel tax exemption form]===== | |
| − | =====[http://statgen.us/files/ | + | |
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=====[https://www.mdc-berlin.de/directions Direction to the MDC Campus]===== | =====[https://www.mdc-berlin.de/directions Direction to the MDC Campus]===== | ||
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=====Direction to the classroom===== | =====Direction to the classroom===== | ||
Location: | Location: | ||
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===Course Instructors=== | ===Course Instructors=== | ||
The organizers and instructors for the course are Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne). | The organizers and instructors for the course are Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne). | ||
| − | [[File: | + | [[File:2016_10_Instructors.jpg|300x402px|link=|none]] |
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| + | ===Course Participants=== | ||
| + | [[File:2016_10_Participants.jpg|500px|link=|none]] | ||
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===Downloads for Course=== | ===Downloads for Course=== | ||
| − | ::* Alohomora ([http://gmc.mdc-berlin.de/alohomora/alohomora_v0. | + | ::* 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/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Data Set] |
::* [https://statgen.research.bcm.edu/files/software/igv.jar igv.jar] | ::* [https://statgen.research.bcm.edu/files/software/igv.jar igv.jar] | ||
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/data/IGVexercise_BAM.zip BAM File] |
===Commands for Computer Exercises=== | ===Commands for Computer Exercises=== | ||
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/commands/annotation.txt Functional Annotation] |
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/commands/gemini.txt Gemini] |
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/commands/rarepedsim.txt RarePedSim] |
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/commands/seqlinkage.txt SEQLinkage] |
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/commands/vat.txt Variant Assocaition Tools] |
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/commands/vmt.txt Variant Mendelian Tools] |
===Exercise Output=== | ===Exercise Output=== | ||
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/files/VMT_screenResults_9_11_15.pdf Variant Mendelian Tools] |
===Course Slides=== | ===Course Slides=== | ||
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/auth/Berlin-2016-10-lectures.pdf download] |
===Data Sets=== | ===Data Sets=== | ||
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Alohomora] |
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/data/annotation.tar.gz Functional Annotation] |
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/data/gemini.tar.gz Gemini] |
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/data/genehunter.tar.gz GeneHunter] |
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/data/IGVexercise_BAM.zip IGV BAM] |
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/data/linkage.tar.gz Linkage] |
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/data/merlin.tar.gz Merlin] |
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/data/rarepedsim.tar.gz RarePedSim] |
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/data/seqlinkage.tar.gz SEQLinkage] |
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/data/slink.tar.gz SLINK] |
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/data/superlink.zip Superlink] |
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/data/vat.tar.gz Variant Association Tools] |
| − | ::* [https://statgen.research.bcm.edu/files/ | + | ::* [https://statgen.research.bcm.edu/files/2016/10/data/vmt.tar.gz Variant Mendelian Tools] |
===Software Links=== | ===Software Links=== | ||
Latest revision as of 19:00, 6 December 2016
Contents
- 1 Identifying Genes for Mendelian Traits using Next Generation Sequence Data
- 1.1 October 31-November 4, 2016Max Delbrück Center (MDC) for Molecular MedicineBerlin, Germany
- 1.2 Course Instructors
- 1.3 Course Participants
- 1.4 Downloads for Course
- 1.5 Commands for Computer Exercises
- 1.6 Exercise Output
- 1.7 Course Slides
- 1.8 Data Sets
- 1.9 Software Links
- 1.10 Databases
- 1.11 Bioinformatic Tools
Identifying Genes for Mendelian Traits using Next Generation Sequence Data
October 31-November 4, 2016
Max Delbrück Center (MDC) for Molecular Medicine
Berlin, Germany
The second annual Identifying Genes for Mendelian Traits using Next Generation Sequence Data Course will be held at the MDC in Berlin from October 31-November 4, 2016. 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
Click here for course schedule
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).
Course Participants
Downloads for Course
Commands for Computer Exercises
Exercise Output
Course Slides
Data Sets
Software Links
Databases
Bioinformatic Tools
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 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
