=====[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]==========[https://www.mdc-berlin.de/directions Direction to the MDC Campus]==========Direction to the classroom=====Location:
:: MDC - communication center (Building C83 on the [httpshttp://statgenwww.researchcampus-berlin-buch.bcm.edude/filesen/2016location/10/Berlin_NGS_Mendelian_Course_Application_2016Campus Map]):: Room Axion 2 The building is red and stands across the street from the campus bus stop and the blue bear.[[File:MDC_C.html Click here jpg|none|300x300px]]===Course Instructors===The organizers and instructors for the application formcourse are Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne).[[File:2016_10_Instructors.jpg|300x402px|link=|none]]
[https://statgen.research.bcm.edu/files/2016/10/Berlin_NGS_Mendelian_flyer_2016.pdf Click here for course flyer] (please post and distribute)
===Course Participants===[[File:2016_10_Participants.jpg|500px|link=|none]] ===Downloads for Course===::* 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/software/igv.jar igv.jar]::* [https://statgen.research.bcm.edu/files/2016/10/data/IGVexercise_BAM.zip BAM File] ===Commands for Computer Exercises===::* [https://statgen.research.bcm.edu/files/2016/10/commands/annotation.txt Functional Annotation]::* [https://statgen.research.bcm.edu/files/2016/10/commands/gemini.txt Gemini]::* [https://statgen.research.bcm.edu/files/2016/10/commands/rarepedsim.txt RarePedSim]::* [https://statgen.research.bcm.edu/files/2016/10/commands/seqlinkage.txt SEQLinkage]::* [https://statgen.research.bcm.edu/files/2016/10/commands/vat.txt Variant Assocaition Tools]::* [https://statgen.research.bcm.edu/files/2016/10/commands/vmt.txt Variant Mendelian Tools] ===Exercise Output===::* [https://statgen.research.bcm.edu/files/2016/10/files/VMT_screenResults_9_11_15.pdf Variant Mendelian Tools] ===Course Slides===::* [https://statgen.research.bcm.edu/files/2016/10/auth/Berlin-2016-10-lectures.pdf download] ===Data Sets===::* [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Alohomora]::* [https://statgen.research.bcm.edu/files/2016/10/data/annotation.tar.gz Functional Annotation]::* [https://statgen.research.bcm.edu/files/2016/10/data/gemini.tar.gz Gemini]::* [https://statgen.research.bcm.edu/files/2016/10/data/genehunter.tar.gz GeneHunter]::* [https://statgen.research.bcm.edu/files/2016/10/data/IGVexercise_BAM.zip IGV BAM]::* [https://statgen.research.bcm.edu/files/2016/10/data/linkage.tar.gz Linkage]::* [https://statgen.research.bcm.edu/files/2016/10/data/merlin.tar.gz Merlin]::* [https://statgen.research.bcm.edu/files/2016/10/data/rarepedsim.tar.gz RarePedSim]::* [https://statgen.research.bcm.edu/files/2016/10/data/seqlinkage.tar.gz SEQLinkage]::* [https://statgen.research.bcm.edu/files/2016/10/data/slink.tar.gz SLINK]::* [https://statgen.research.bcm.edu/files/2016/10/data/superlink.zip Superlink]::* [https://statgen.research.bcm.edu/files/2016/10/data/vat.tar.gz Variant Association Tools]::* [https://statgen.research.bcm.edu/files/2016/10/data/vmt.tar.gz Variant Mendelian Tools] ===Software Links===::* [http://gmc.mdc-berlin.de/alohomora/ Alohomora]::* [http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/fastlink.html FASTLINK]::* [https://gemini.readthedocs.org/ Gemini]::* [http://www.broad.mit.edu/ftp/distribution/software/genehunter/ GeneHunter]::* [http://www.homozygositymapper.org/ Homozygosity Mapper]::* [https://www.broadinstitute.org/igv/ Integrative Genome Viewer (IGV)] [https://statgen.research.bcm.edu/files/igv.jar [download jar]]::* [http://www.jurgott.org/linkage/LinkagePC.html LINKAGE]::* [http://csg.sph.umich.edu/abecasis/Merlin/ MERLIN]::* [http://bioinformatics.org/simped/rare/ RarePedSim]::* [http://www.bioinformatics.org/seqlink/ SEQLinkage]::* [http://www.jurgott.org/linkage/SLINK.htm SLINK/MSIM]::* [http://bioinfo.cs.technion.ac.il/superlink-online/index-working2.shtml SUPERLINK]::* [http://varianttools.sourceforge.net/Association/HomePage Variant Association Tools]::* [http://statgen.research.bcm.edu/VMT Variant Mendelian Tools] ===Databases===::* [http://exac.broadinstitute.org/ ExAC] ===Bioinformatic Tools===::* [http://cadd.gs.washington.edu/score CADD]::* [http://fathmm.biocompute.org.uk/inherited.html FATHMM]::* [http://mendel.stanford.edu/SidowLab/downloads/gerp/ GERP]::* [http://www.genetics.wustl.edu/jflab/lrt_query.html LRT]::* [http://www.mutationtaster.org/ChrPos.html Mutation Taster]::* [http://genome.ucsc.edu/cgi-bin/hgGateway Nucleotide Conservation]::* [http://compgen.bscb.cornell.edu/phast/ PhyloP]::* [http://genetics.bwh.harvard.edu/pph2/bgi.shtml PolyPhen-2]::* [http://provean.jcvi.org/genome_submit_2.php?species=human PROVEAN and SIFT]::* [http://grch37.ensembl.org/Homo_sapiens/Tools/VEP VEP] [https://www.mdc-berlin.de/directions Click here for maps and directions to the MDC]<br data-attributes="%20/">[http://www.bbb-berlin.de/en/gaestehaeuser.html Click here for the information on MDC Housing]<br data-attributes="%20/">[http://www.visitberlin.de/en Click here for Berlin tourist information]<br data-attributes/>[https://www.facebook.com/statgencourses/?ref="%20aymt_homepage_panel Click here and like us on Facebook]<br /">[https://statgen.research.bcm.edu/2015SeptMDCindex.php/view 2015SeptMDC Click here for photos and datasets from the Analysis of Next Generation Sequence Data Mendelian Traits - Berlin: September 2015]<br data-attributes="%20/">[https://statgen.research.bcm.edu/2015JuneMDCindex.php/view 2015JuneMDC Click here for photos and datasets from the Genetic Association Course - Berlin: June 2015]<br data-attributes="%20/">[https://statgen.research.bcm.edu/2015MarchMDCindex.php/view 2015MarchMDC Click here for photos and datasets from the Analysis of Next Generation Sequence Data Complex Traits - Berlin: March 2015]<br data/>[http://portal.ccg.uni-attributeskoeln.de/ccg/index.php?id="%2089 Click here for photos and datasets from the Genetic Association Course - Berlin: June 2015]<br /">[http://portal.ccg.uni-koeln.de/ccg/researchindex.php?id=88 Click here for photos and datasets from the Complex Trait Analysis of NGS Data Course - Berlin: March 2015]<br /stat>[http://portal.ccg.uni-gen-bioinformaticskoeln.de/coursesccg/ngsdac2014index.html php?id=87 Click here for photos and datasets from the Next Generation Sequence Data Analysis Course - Berlin: June 2014]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2014index.html php?id=86 Click here for photos and datasets from the Genetic Association Course - Berlin: March 2014]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2013index.html php?id=85 Click here for photos and datasets from the Genetic Association Course - Berlin: June 2013]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2012index.html php?id=84 Click here for photos and datasets from the Basic Gene Mapping Course - Berlin: November 2012]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2012index.html php?id=83 Click here for photos from the Genetic Association Course - Berlin: July 2012]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2011index.html php?id=81 Click here for photos from the Basic Gene Mapping Course - Berlin: November 2011]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2011index.html php?id=80 Click here for photos from the Genetic Association Course - Berlin: July 2011]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2010index.html php?id=63 Click here for photos from the Basic Gene Mapping Course - Berlin: October 2010]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2010index.html php?id=62 Click here for photos from the Genetic Association Course - Berlin: May 2010]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2009index.html php?id=90 Click here for photos from the Basic Gene Mapping Course - Berlin: November 2009]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2008index.html php?id=91 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2008]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2007index.html php?id=92 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2007]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2006index.html php?id=93 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2006]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2005index.html php?id=94 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2005]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2004index.html php?id=95 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2004]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2003index.html php?id=96 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2003]