The organizers and instructors for the course are Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne).
[[File:2017-06NGCM-Instructors.jpg|none|224x300px300px]]
===Course Participants===
[[File:2017-NGCM-Participants.jpg|none|500px]]<br />[[File:2017-NGCM-All.jpg|none|500px]]
===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]
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]
X11 support
::* [https://sourceforge.net/projects/xming/ Xming (for Windows)]
::* [https://www.xquartz.org/index.html XQuartz (for macOS)]
Gemini
::* [https://drive.google.com/file/d/0B2pJ9cgevF3sTS1DeGxYalFTN00/view Bam files for exercise]
[https://statgen.research.bcm.edu/files/2017/09/img/Mendelian.tar.bz2 Virtualbox Image] of Course Computers (requires [https://www.virtualbox.org/ VirtualBox])
===Commands for Computer Exercises===
::* [https://statgen.research.bcm.edu/files/2017/09/commands/annovar-functional_annotation.txt Annovar - Functional Annotation]
::* [https://statgen.research.bcm.edu/files/2017/09/commands/annovar-variant_filtering.txt Annovar - Variant Filtering]
::* [https://statgen.research.bcm.edu/files/2017/09/commands/gemini.txt Gemini]
::* [https://statgen.research.bcm.edu/files/2016/10/commands/seqlinkage.txt SEQLinkage]
::* [https://statgen.research.bcm.edu/files/2017/09/commands/vat.txt Variant Assocaition Tools]
::* [https://statgen.research.bcm.edu/files/2016/10/commands/vmt.txt Variant Mendelian Tools]
===Data Sets===
::* [https://statgen.research.bcm.edu/files/2016/10/data/alohomora.zip Alohomora]
::* [https://statgen.research.bcm.edu/files/2017/09/data/annovar.tar.gz Annovar]
::* [https://statgen.research.bcm.edu/files/2017/09/data/gemini.tar.gz Gemini]
::* [https://statgen.research.bcm.edu/files/2016/10/data/genehunter.tar.gz GeneHunter]
::* [https://statgen.research.bcm.edu/files/2017/09/data/igv_exercise.zip IGV BAM and VCF files]
::* [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/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://annovar.openbioinformatics.org/en/latest/user-guide/download/ ANNOVAR]
::* [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/software/igv/igv-2.3.97.jar [download jar]]
::* [http://www.jurgott.org/linkage/LinkagePC.html LINKAGE]
::* [http://csg.sph.umich.edu/abecasis/Merlin/ MERLIN]
::* [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]
::* [http://gnomad.broadinstitute.org/ gnomAD]
===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]
===Other Links===
::* [https://www.acmg.net/docs/Standards_Guidelines_for_the_Interpretation_of_Sequence_Variants.pdf ACMG Standards and Guidelines for the Interpretation of Sequence Variants]