Changes

NGSMendelian2017

435 bytes added, 16:53, 15 June 2018
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/20162017/1009/commands/vat.txt Variant Assocaition Tools]
::* [https://statgen.research.bcm.edu/files/2016/10/commands/vmt.txt Variant Mendelian Tools]
::* [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 REBUILD THIS] -->
::* [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]
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