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==Identifying Genes for Mendelian Traits using Next Generation Sequence Data==
Sept 28-Oct 2, 2015, Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany
===General Information===
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, PhyloP, 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, identification of causal variants using filter approaches, variant annotation, evaluation of deleterious effects of variants and their functionality
=====[https://statgen.research.bcm.edu/files/201509/Berlin_NGS_schedule_8_26_15_2015.pdf Course Schedule]=====
=====[[Media:BerlinHotelExemption.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 [http://www.campus-berlin-buch.de/en/location/ Campus 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.jpg|none|300x300px]]
===Course Instructors===
The organizers and instructors for the course are Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne).
[[File:2015JuneInstructors.jpg|none]]
===Pictures from the Course===
[[File:2015SeptemberCourseParticipants.jpg|none|400x267px]]
===Downloads for Course===
::* Alohomora ([http://gmc.mdc-berlin.de/alohomora/alohomora_v0.33-linux.tar.gz Linux] [http://gmc.mdc-berlin.de/alohomora/alohomora_v0.33-win32.zip Windows])
::* [https://statgen.research.bcm.edu/files/201509/data/alohomora.zip Data Set]
::* [https://statgen.research.bcm.edu/files/software/igv.jar IGV.jar]
::* [https://statgen.research.bcm.edu/files/201509/data/IGVexercise_BAM.zip BAM File]
===Commands for Computer Exercises===
::* [https://statgen.research.bcm.edu/files/2015/09/commands/annotation.txt Functional Annotation]
::* [https://statgen.research.bcm.edu/files/2015/09/commands/gemini.txt Gemini]
::* [https://statgen.research.bcm.edu/files/2015/09/commands/rarepedsim.txt RarePedSim]
::* [https://statgen.research.bcm.edu/files/2015/09/commands/seqlinkage.txt SEQLinkage]
::* [https://statgen.research.bcm.edu/files/2015/09/commands/vat.txt Variant Assocaition Tools]
::* [https://statgen.research.bcm.edu/files/2015/09/commands/vmt.txt Variant Mendelian Tools]
===Exercise Output===
::* [https://statgen.research.bcm.edu/files/201509/files/VMT_screenResults_9_11_15.pdf Variant Mendelian Tools]
===Course Slides===
::* [https://statgen.research.bcm.edu/files/201509/files/berlin_book_lectures_only_2015_10_13.pdf download]
===Data Sets===
::* [https://statgen.research.bcm.edu/files/2015/09/data/alohomora.zip Alohomora]
::* [https://statgen.research.bcm.edu/files/2015/09/data/annotation.tar.gz Functional Annotation]
::* [https://statgen.research.bcm.edu/files/2015/09/data/gemini.tar.gz Gemini]
::* [https://statgen.research.bcm.edu/files/2015/09/data/genehunter.tar.gz GeneHunter]
::* [https://statgen.research.bcm.edu/files/2015/09/data/IGVexercise_BAM.zip IGV BAM]
::* [https://statgen.research.bcm.edu/files/2015/09/data/linkage.tar.gz Linkage]
::* [https://statgen.research.bcm.edu/files/2015/09/data/merlin.tar.gz Merlin]
::* [https://statgen.research.bcm.edu/files/2015/09/data/rarepedsim.tar.gz RarePedSim]
::* [https://statgen.research.bcm.edu/files/2015/09/data/seqlinkage.tar.gz SEQLinkage]
::* [https://statgen.research.bcm.edu/files/2015/09/data/slink.tar.gz SLINK]
::* [https://statgen.research.bcm.edu/files/2015/09/data/superlink.zip Superlink]
::* [https://statgen.research.bcm.edu/files/2015/09/data/vat.tar.gz Variant Association Tools]
::* [https://statgen.research.bcm.edu/files/2015/09/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]