Difference between revisions of "NGSMendelian2016"

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(Created page with "__NOTITLE__ =Identifying Genes for Mendelian Traits using Next Generation Sequence Data= ===October 31-November 4, 2016<br data-attributes="%20/">Max Delbrück Center (MDC) f...")
 
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For additional information on the course please contact [mailto:sleal@bcm.edu?subject=Genetic%20Association%20Course%2C%20Berlin%202015 Suzanne Leal]:
 
For additional information on the course please contact [mailto:sleal@bcm.edu?subject=Genetic%20Association%20Course%2C%20Berlin%202015 Suzanne Leal]:
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Application Deadline August 1, 2016
 
  
 
* email: [mailto:sleal@bcm.edu;suzannemleal@gmail.com?subject=Genetic%20Association%20Course%20Berlin%202016 sleal@bcm.edu]
 
* email: [mailto:sleal@bcm.edu;suzannemleal@gmail.com?subject=Genetic%20Association%20Course%20Berlin%202016 sleal@bcm.edu]
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[https://statgen.research.bcm.edu/files/2016/10/Schedule_NGS_Mendelian_2016.pdf Click here for course schedule]
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=====[https://statgen.research.bcm.edu/files/2016/10/Schedule_NGS_Mendelian_2016.pdf Click here for course schedule]=====
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=====[http://statgen.us/files/2016/10/BerlinHotelTaxExemptionForm.pdf Link to Berlin hotel tax exemption form]=====
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=====[https://www.mdc-berlin.de/directions Direction to the MDC Campus]=====
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=====Direction to the classroom=====
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Location:
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:: MDC - communication center (Building C83 on the [http://www.campus-berlin-buch.de/en/location/ Campus Map])
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:: Room Axion 2&nbsp;
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The building is red and stands across the street from the campus bus stop and the blue bear.
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[[File:MDC_C.jpg|none|300x300px]]
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===Course Instructors===
 +
The organizers and instructors for the course are Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne).
 +
[[File:2016_10_Instructors.jpg|300x402px|link=|none]]
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===Course Participants===
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[[File:2016_10_Participants.jpg|500px|link=|none]]
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===Downloads for Course===
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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])
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::* [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Data Set]
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::* [https://statgen.research.bcm.edu/files/software/igv.jar igv.jar]
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::* [https://statgen.research.bcm.edu/files/2016/10/data/IGVexercise_BAM.zip BAM File]
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===Commands for Computer Exercises===
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::* [https://statgen.research.bcm.edu/files/2016/10/commands/annotation.txt Functional Annotation]
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::* [https://statgen.research.bcm.edu/files/2016/10/commands/gemini.txt Gemini]
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::* [https://statgen.research.bcm.edu/files/2016/10/commands/rarepedsim.txt RarePedSim]
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::* [https://statgen.research.bcm.edu/files/2016/10/commands/seqlinkage.txt SEQLinkage]
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::* [https://statgen.research.bcm.edu/files/2016/10/commands/vat.txt Variant Assocaition Tools]
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::* [https://statgen.research.bcm.edu/files/2016/10/commands/vmt.txt Variant Mendelian Tools]
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===Exercise Output===
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::* [https://statgen.research.bcm.edu/files/2016/10/files/VMT_screenResults_9_11_15.pdf Variant Mendelian Tools]
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===Course Slides===
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::* [https://statgen.research.bcm.edu/files/2016/10/auth/Berlin-2016-10-lectures.pdf download]
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===Data Sets===
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::* [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Alohomora]
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::* [https://statgen.research.bcm.edu/files/2016/10/data/annotation.tar.gz Functional Annotation]
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::* [https://statgen.research.bcm.edu/files/2016/10/data/gemini.tar.gz Gemini]
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::* [https://statgen.research.bcm.edu/files/2016/10/data/genehunter.tar.gz GeneHunter]
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::* [https://statgen.research.bcm.edu/files/2016/10/data/IGVexercise_BAM.zip IGV BAM]
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::* [https://statgen.research.bcm.edu/files/2016/10/data/linkage.tar.gz Linkage]
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::* [https://statgen.research.bcm.edu/files/2016/10/data/merlin.tar.gz Merlin]
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::* [https://statgen.research.bcm.edu/files/2016/10/data/rarepedsim.tar.gz RarePedSim]
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::* [https://statgen.research.bcm.edu/files/2016/10/data/seqlinkage.tar.gz SEQLinkage]
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::* [https://statgen.research.bcm.edu/files/2016/10/data/slink.tar.gz SLINK]
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::* [https://statgen.research.bcm.edu/files/2016/10/data/superlink.zip Superlink]
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::* [https://statgen.research.bcm.edu/files/2016/10/data/vat.tar.gz Variant Association Tools]
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::* [https://statgen.research.bcm.edu/files/2016/10/data/vmt.tar.gz Variant Mendelian Tools]
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===Software Links===
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::* [http://gmc.mdc-berlin.de/alohomora/ Alohomora]
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::* [http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/fastlink.html FASTLINK]
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::* [https://gemini.readthedocs.org/ Gemini]
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::* [http://www.broad.mit.edu/ftp/distribution/software/genehunter/ GeneHunter]
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::* [http://www.homozygositymapper.org/ Homozygosity Mapper]
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::* [https://www.broadinstitute.org/igv/ Integrative Genome Viewer (IGV)] [https://statgen.research.bcm.edu/files/igv.jar [download jar]]
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::* [http://www.jurgott.org/linkage/LinkagePC.html LINKAGE]
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::* [http://csg.sph.umich.edu/abecasis/Merlin/ MERLIN]
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::* [http://bioinformatics.org/simped/rare/ RarePedSim]
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::* [http://www.bioinformatics.org/seqlink/ SEQLinkage]
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::* [http://www.jurgott.org/linkage/SLINK.htm SLINK/MSIM]
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::* [http://bioinfo.cs.technion.ac.il/superlink-online/index-working2.shtml SUPERLINK]
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::* [http://varianttools.sourceforge.net/Association/HomePage Variant Association Tools]
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::* [http://statgen.research.bcm.edu/VMT Variant Mendelian Tools]
  
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[https://statgen.research.bcm.edu/files/2016/10/Berlin_NGS_Mendelian_Course_Application_2016.html Click here for the application form]
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===Databases===
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::* [http://exac.broadinstitute.org/ ExAC]
  
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[https://statgen.research.bcm.edu/files/2016/10/Berlin_NGS_Mendelian_flyer_2016.pdf Click here for course flyer] (please post and distribute)
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===Bioinformatic Tools===
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::* [http://cadd.gs.washington.edu/score CADD]
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::* [http://fathmm.biocompute.org.uk/inherited.html FATHMM]
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::* [http://mendel.stanford.edu/SidowLab/downloads/gerp/ GERP]
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::* [http://www.genetics.wustl.edu/jflab/lrt_query.html LRT]
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::* [http://www.mutationtaster.org/ChrPos.html Mutation Taster]
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::* [http://genome.ucsc.edu/cgi-bin/hgGateway Nucleotide Conservation]
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::* [http://compgen.bscb.cornell.edu/phast/ PhyloP]
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::* [http://genetics.bwh.harvard.edu/pph2/bgi.shtml PolyPhen-2]
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::* [http://provean.jcvi.org/genome_submit_2.php?species=human PROVEAN and SIFT]
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::* [http://grch37.ensembl.org/Homo_sapiens/Tools/VEP VEP]
  
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[https://www.mdc-berlin.de/directions Click here for maps and directions to the MDC]<br data-attributes="%20/">
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[https://www.mdc-berlin.de/directions Click here for maps and directions to the MDC]<br />
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[http://www.bbb-berlin.de/en/gaestehaeuser.html Click here for the information on MDC Housing]<br data-attributes="%20/">
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[http://www.bbb-berlin.de/en/gaestehaeuser.html Click here for the information on MDC Housing]<br />
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[http://www.visitberlin.de/en Click here for Berlin tourist information]<br data-attributes="%20/">
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[http://www.visitberlin.de/en Click here for Berlin tourist information]<br />
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[https://statgen.research.bcm.edu/2015SeptMDC/view Click here for photos and datasets from the Analysis of Next Generation Sequence Data Mendelian Traits - Berlin: September 2015]<br data-attributes="%20/">
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[https://www.facebook.com/statgencourses/?ref=aymt_homepage_panel Click here and like us on Facebook]<br />
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[https://statgen.research.bcm.edu/2015JuneMDC/view Click here for photos and datasets from the Genetic Association Course - Berlin: June 2015]<br data-attributes="%20/">
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[https://statgen.research.bcm.edu/index.php/2015SeptMDC Click here for photos and datasets from the Analysis of Next Generation Sequence Data Mendelian Traits - Berlin: September 2015]<br />
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[https://statgen.research.bcm.edu/2015MarchMDC/view Click here for photos and datasets from the Analysis of Next Generation Sequence Data Complex Traits - Berlin: March 2015]<br data-attributes="%20/">
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[https://statgen.research.bcm.edu/index.php/2015JuneMDC Click here for photos and datasets from the Genetic Association Course - Berlin: June 2015]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/ngsdac2014.html Click here for photos and datasets from the Next Generation Sequence Data Analysis Course - Berlin: June 2014]<br data-attributes="%20/">
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[https://statgen.research.bcm.edu/index.php/2015MarchMDC Click here for photos and datasets from the Analysis of Next Generation Sequence Data Complex Traits - Berlin: March 2015]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2014.html Click here for photos and datasets from the Genetic Association Course - Berlin: March 2014]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=89 Click here for photos and datasets from the Genetic Association Course - Berlin: June 2015]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2013.html Click here for photos and datasets from the Genetic Association Course - Berlin: June 2013]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=88 Click here for photos and datasets from the Complex Trait Analysis of NGS Data Course - Berlin: March 2015]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2012.html Click here for photos and datasets from the Basic Gene Mapping Course - Berlin: November 2012]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=87 Click here for photos and datasets from the Next Generation Sequence Data Analysis Course - Berlin: June 2014]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2012.html Click here for photos from the Genetic Association Course - Berlin: July 2012]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=86 Click here for photos and datasets from the Genetic Association Course - Berlin: March 2014]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2011.html Click here for photos from the Basic Gene Mapping Course - Berlin: November 2011]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=85 Click here for photos and datasets from the Genetic Association Course - Berlin: June 2013]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2011.html Click here for photos from the Genetic Association Course - Berlin: July 2011]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=84 Click here for photos and datasets from the Basic Gene Mapping Course - Berlin: November 2012]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2010.html Click here for photos from the Basic Gene Mapping Course - Berlin: October 2010]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=83 Click here for photos from the Genetic Association Course - Berlin: July 2012]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2010.html Click here for photos from the Genetic Association Course - Berlin: May 2010]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=81 Click here for photos from the Basic Gene Mapping Course - Berlin: November 2011]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2009.html Click here for photos from the Basic Gene Mapping Course - Berlin: November 2009]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=80 Click here for photos from the Genetic Association Course - Berlin: July 2011]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2008.html Click here for photos from the Basic Gene Mapping Course - Berlin: July 2008]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=63 Click here for photos from the Basic Gene Mapping Course - Berlin: October 2010]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2007.html Click here for photos from the Basic Gene Mapping Course - Berlin: July 2007]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=62 Click here for photos from the Genetic Association Course - Berlin: May 2010]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2006.html Click here for photos from the Basic Gene Mapping Course - Berlin: July 2006]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=90 Click here for photos from the Basic Gene Mapping Course - Berlin: November 2009]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2005.html Click here for photos from the Basic Gene Mapping Course - Berlin: July 2005]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=91 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2008]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2004.html Click here for photos from the Basic Gene Mapping Course - Berlin: July 2004]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=92 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2007]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2003.html Click here for photos from the Basic Gene Mapping Course - Berlin: July 2003]
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=93 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2006]<br />
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=94 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2005]<br />
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=95 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2004]<br />
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=96 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2003]

Latest revision as of 19:00, 6 December 2016

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.

MDC C.jpg

Course Instructors

The organizers and instructors for the course are Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne).

2016 10 Instructors.jpg


Course Participants

2016 10 Participants.jpg

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

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