View source for 2015MarchMDC

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==Complex Trait Analysis of Next Generation Sequence Data==
March 23-27, 2015, Max Delbrück Center (MDC) for Molecular Medicine, Berlin, Germany

===Course Participants===
[[File:2015MarchParticipantsCloseup.JPG|center|frame]]

===General Information===
The goal of the course is to teach the course participants both the theory and application of methods to analyze next generation sequence (NGS) data for human complex traits. Attendees will learn how to design studies, call variants from NGS data, analysis of population- and trio- based sequence data and evaluation of variant functionality. Analyses will include performing complex trait rare variant association analysis for population and trio data. Exercises will be carried out using a variety of computer programs (GATK, IGV, Polyphen2, PSEQ, SEQPower, and Variant Association Tools (VAT)). TOPICS will be include: sequence alignment, calling variants from NGS data, quality control of NGS data, association testing framework for quantitative and qualitative traits (fixed effects, random effects and mixed models), rare variant association methods, estimating power and sample size for rare variant association studies, imputation of rare variants and their analysis, detecting putative causal variants for Mendelian traits and evaluating variant functionality.

=====[[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.
===Course Instructors===
The instructors for the course are Laurent Francioli (University Medical Center Utrecht), Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne).

[[File:2015MarchCourseInstructors.JPG|center|frame]]

===[[2015-march-berlin-commands|Commands for Computer Exercises]]===
===Data-sets Used During the Course===
::* [http://statgen.us/uploads/annotation.tar.bz2 Annotation exercise]
::* [http://statgen.us/uploads/GATK.tar.bz2 GATK exercise]
::* [http://statgen.us/uploads/PSEQ.tar.bz2 PLINKSEQ exercise]
::* [http://statgen.us/uploads/popgen.tar.bz2 PopGen exercise]
::* [http://statgen.us/uploads/regression.tar.bz2 Regression Intro exercise]
::* [http://statgen.us/uploads/SEQPower.tar.bz2 SEQPower exercise]
::* [http://statgen.us/uploads/VAT.tar.bz2 Variant Association Tools exercise]
In order to obtain a particular data set, please follow the following steps:
::# Download the respective data archive file (''*.tar.bz2'') and place it into an appropriate directory.
::# At the command prompt (aka shell or terminal), make this directory the working directory by using the ''cd'' command.
::# Extract the data files by typing ''tar xjvf'' and adding the name of the archive file. The data files will then be in a corresponding subdirectory.
::# Change to this subdirectory (''cd'' command) and proceed with the exercise.

===Software Links===
::* [https://www.broadinstitute.org/gatk/ GATK]
::* [http://www.broadinstitute.org/igv/ IGV]
::* [http://genetics.bwh.harvard.edu/pph2/ Polyphen2]
::* [https://atgu.mgh.harvard.edu/plinkseq/ PSEQ]
::* [http://www.bioinformatics.org/spower/start SEQPower]
::* [http://varianttools.sf.net/VAT Variant Association Tools]