Difference between revisions of "ComplexNGS2016"

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(→‎July 4-8, 2016Max Delbrück Center (MDC) for Molecular MedicineBerlin, Germany)
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The instructors for the course are [https://www.bcm.edu/research/labs/center-for-statistical-genetics/ Suzanne Leal] (Baylor College of Medicine) and [http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/ Michael Nothnagel] (University of Cologne).
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=====[http://statgen.us/files/2015/09/BerlinHotelTaxExemptionForm.pdf Link to Berlin hotel tax exemption form]=====
  
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=====[https://www.mdc-berlin.de/directions Direction to the MDC Campus]=====
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===Direction to the classroom===
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Location:
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:: MDC - communication center (Building C83 on the [http://www.campus-berlin-buch.de/en/location/ Campus Map])
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:: Room Dendrit 2/3
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[[File:MDC_C.jpg|none|250x250px]]
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The building is red and stands across the street from the campus bus stop and the blue bear.
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The instructors for the course are [https://www.bcm.edu/research/labs/center-for-statistical-genetics/ Suzanne Leal] (Baylor College of Medicine) and [http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/ Michael Nothnagel] (University of Cologne).
  
 
The cost of the 5 day course is 975 EUR for researchers from an academic institution, and 1,950 EUR for individuals from private (for profit) companies. This fee covers tuition, Monday evening wine and cheese party and course related expenses (handouts, etc.) but not room, board or meals. Inexpensive housing is available for course participants at the MDC and nearby hotels. The maximum number of participants is 40.
 
The cost of the 5 day course is 975 EUR for researchers from an academic institution, and 1,950 EUR for individuals from private (for profit) companies. This fee covers tuition, Monday evening wine and cheese party and course related expenses (handouts, etc.) but not room, board or meals. Inexpensive housing is available for course participants at the MDC and nearby hotels. The maximum number of participants is 40.
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* Tel: +1 (713) 798-4011
 
* Tel: +1 (713) 798-4011
 
* Fax: +1 (713) 798-4012
 
* Fax: +1 (713) 798-4012
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 +
===Course Instructors===
 +
The organizers and instructors for the course are Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne).
 +
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[[File:2016-07_instructors.jpg|none|200x308px]]
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===Course Participants===
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[[File:2016-07_participants.jpg|none|480x209px]]
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===[[2016-july-berlin-commands|Commands for Exercises]]===
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===[https://statgen.research.bcm.edu/files/2016/07/auth/Berlin_July_2016_LectureOnly.pdf Course Slides]===
  
 
===Data-sets Used During the Course===
 
===Data-sets Used During the Course===
 
::* [http://statgen.us/files/2016/07/annotation.tar.bz2 Annotation exercise]
 
::* [http://statgen.us/files/2016/07/annotation.tar.bz2 Annotation exercise]
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::* [http://statgen.us/uploads/GATK.tar.bz2 GATK exercise]
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::* [http://statgen.us/files/2016/07/gatk.tar.bz2 GATK/IGV exercise]
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::* [http://statgen.us/uploads/PSEQ.tar.bz2 PLINKSEQ exercise]
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::* [http://statgen.us/files/2015/09/data/IGVexercise_BAM.zip IGV exercise]
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::* [http://statgen.us/files/2016/07/pseq.tar.bz2 PSEQ exercise]
 
::* [http://statgen.us/files/2016/07/popgen.tar.bz2 PopGen exercise]
 
::* [http://statgen.us/files/2016/07/popgen.tar.bz2 PopGen exercise]
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::* [http://statgen.us/uploads/regression.tar.bz2 Regression Intro exercise]
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::* [http://statgen.us/files/2016/07/regression.tar.bz2 Regression exercise]
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::* [http://statgen.us/uploads/SEQPower.tar.bz2 SEQPower exercise]
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::* [http://statgen.us/files/2016/07/seqpower.tar.bz2 SEQPower exercise]
 
::* [http://statgen.us/files/2016/07/vat.tar.bz2 Variant Association Tools exercise]
 
::* [http://statgen.us/files/2016/07/vat.tar.bz2 Variant Association Tools exercise]
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In order to obtain a particular data set, please follow the following steps:
 
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::# Download the respective data archive file (''*.tar.bz2'') and place it into an appropriate directory.
 
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::# At the command prompt (aka shell or terminal), make this directory the working directory by using the ''cd'' command.
 
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::# 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.
 
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::# Change to this subdirectory (''cd'' command) and proceed with the exercise.
 
  
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===Result Files===
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::* [http://statgen.us/files/2016/07/gatk_results.tar.gz GATK/IGV exercise]
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===Software Links===
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::* [https://www.broadinstitute.org/gatk/ GATK]
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::* [http://www.broadinstitute.org/igv/ IGV]
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::* [https://atgu.mgh.harvard.edu/plinkseq/ PSEQ]
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::* [https://www.r-project.org/ R]
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::* [http://www.bioinformatics.org/spower/start SEQPower]
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::* [http://varianttools.sf.net/VAT Variant Association Tools]
  
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===Bioinformatic Tools===
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::* [http://cadd.gs.washington.edu/score CADD]
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::* [http://fathmm.biocompute.org.uk/inherited.html FATHMM]
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::* [http://mendel.stanford.edu/SidowLab/downloads/gerp/ GERP]
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::* [http://www.genetics.wustl.edu/jflab/lrt_query.html LRT]
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::* [http://www.mutationtaster.org/ChrPos.html Mutation Taster]
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::* [http://genome.ucsc.edu/cgi-bin/hgGateway Nucleotide Conservation]
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::* [http://compgen.bscb.cornell.edu/phast/ PhyloP]
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::* [http://genetics.bwh.harvard.edu/pph2/bgi.shtml PolyPhen-2]
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::* [http://provean.jcvi.org/genome_submit_2.php?species=human PROVEAN and SIFT]
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::* [http://grch37.ensembl.org/Homo_sapiens/Tools/VEP VEP]
  
 
[https://statgen.research.bcm.edu/files/2016/07/schedule_berlin_complex_ngs_2016.pdf Click here for course schedule]
 
[https://statgen.research.bcm.edu/files/2016/07/schedule_berlin_complex_ngs_2016.pdf Click here for course schedule]
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[http://www.bbb-berlin.de/en/gaestehaeuser.html Click here for the information on MDC Housing]<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="%20/">
 
[http://www.visitberlin.de/en Click here for Berlin tourist information]<br data-attributes="%20/">
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[https://statgen.research.bcm.edu/2015SeptMDC/view Click here for photos and datasets from the Analysis of Next Generation Sequence Data Mendelian Traits - Berlin: September 2015]<br data-attributes="%20/">
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[https://www.facebook.com/statgencourses/?ref=aymt_homepage_panel Click here and like us on Facebook]<br />
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[https://statgen.research.bcm.edu/2015JuneMDC/view Click here for photos and datasets from the Genetic Association Course - Berlin: June 2015]<br data-attributes="%20/">
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[https://statgen.research.bcm.edu/index.php/2015SeptMDC Click here for photos and datasets from the Analysis of Next Generation Sequence Data Mendelian Traits - Berlin: September 2015]<br />
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[https://statgen.research.bcm.edu/2015MarchMDC/view Click here for photos and datasets from the Analysis of Next Generation Sequence Data Complex Traits - Berlin: March 2015]<br data-attributes="%20/">
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[https://statgen.research.bcm.edu/index.php/2015JuneMDC Click here for photos and datasets from the Genetic Association Course - Berlin: June 2015]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/ngsdac2014.html Click here for photos and datasets from the Next Generation Sequence Data Analysis Course - Berlin: June 2014]<br data-attributes="%20/">
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[https://statgen.research.bcm.edu/index.php/2015MarchMDC Click here for photos and datasets from the Analysis of Next Generation Sequence Data Complex Traits - Berlin: March 2015]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2014.html Click here for photos and datasets from the Genetic Association Course - Berlin: March 2014]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=89 Click here for photos and datasets from the Genetic Association Course - Berlin: June 2015]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2013.html Click here for photos and datasets from the Genetic Association Course - Berlin: June 2013]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=88 Click here for photos and datasets from the Complex Trait Analysis of NGS Data Course - Berlin: March 2015]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2012.html Click here for photos and datasets from the Basic Gene Mapping Course - Berlin: November 2012]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=87 Click here for photos and datasets from the Next Generation Sequence Data Analysis Course - Berlin: June 2014]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2012.html Click here for photos from the Genetic Association Course - Berlin: July 2012]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=86 Click here for photos and datasets from the Genetic Association Course - Berlin: March 2014]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2011.html Click here for photos from the Basic Gene Mapping Course - Berlin: November 2011]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=85 Click here for photos and datasets from the Genetic Association Course - Berlin: June 2013]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2011.html Click here for photos from the Genetic Association Course - Berlin: July 2011]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=84 Click here for photos and datasets from the Basic Gene Mapping Course - Berlin: November 2012]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2010.html Click here for photos from the Basic Gene Mapping Course - Berlin: October 2010]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=83 Click here for photos from the Genetic Association Course - Berlin: July 2012]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2010.html Click here for photos from the Genetic Association Course - Berlin: May 2010]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=81 Click here for photos from the Basic Gene Mapping Course - Berlin: November 2011]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2009.html Click here for photos from the Basic Gene Mapping Course - Berlin: November 2009]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=80 Click here for photos from the Genetic Association Course - Berlin: July 2011]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2008.html Click here for photos from the Basic Gene Mapping Course - Berlin: July 2008]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=63 Click here for photos from the Basic Gene Mapping Course - Berlin: October 2010]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2007.html Click here for photos from the Basic Gene Mapping Course - Berlin: July 2007]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=62 Click here for photos from the Genetic Association Course - Berlin: May 2010]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2006.html Click here for photos from the Basic Gene Mapping Course - Berlin: July 2006]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=90 Click here for photos from the Basic Gene Mapping Course - Berlin: November 2009]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2005.html Click here for photos from the Basic Gene Mapping Course - Berlin: July 2005]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=91 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2008]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2004.html Click here for photos from the Basic Gene Mapping Course - Berlin: July 2004]<br data-attributes="%20/">
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=92 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2007]<br />
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[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2003.html Click here for photos from the Basic Gene Mapping Course - Berlin: July 2003]
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=93 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2006]<br />
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=94 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2005]<br />
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=95 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2004]<br />
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[http://portal.ccg.uni-koeln.de/ccg/index.php?id=96 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2003]

Latest revision as of 19:23, 4 October 2016

Complex Trait Analysis of Next Generation Sequence Data

July 4-8, 2016
Max Delbrück Center (MDC) for Molecular Medicine
Berlin, Germany

The second annual course on Complex Trait Analysis of Next Generation Sequence Data will be held at the MDC in Berlin from July 4-8, 2016. 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, evaluating variant functionality.


Link to Berlin hotel tax exemption form
Direction to the MDC Campus

Direction to the classroom

Location:

MDC - communication center (Building C83 on the Campus Map)
Room Dendrit 2/3
MDC C.jpg

The building is red and stands across the street from the campus bus stop and the blue bear. The instructors for the course are Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne).

The cost of the 5 day course is 975 EUR for researchers from an academic institution, and 1,950 EUR for individuals from private (for profit) companies. This fee covers tuition, Monday evening wine and cheese party and course related expenses (handouts, etc.) but not room, board or meals. Inexpensive housing is available for course participants at the MDC and nearby hotels. The maximum number of participants is 40.


For additional information on the course please contact Suzanne Leal:

  • email: sleal@bcm.edu
  • Tel: +1 (713) 798-4011
  • Fax: +1 (713) 798-4012

Course Instructors

The organizers and instructors for the course are Suzanne Leal (Baylor College of Medicine) and Michael Nothnagel (University of Cologne).

2016-07 instructors.jpg

Course Participants

2016-07 participants.jpg

Commands for Exercises

Course Slides

Data-sets Used During the Course

Result Files

Software Links

Bioinformatic Tools

Click here for course schedule

Click here for the application form

Click here for course flyer (please post and distribute)

Click here for maps and directions to the MDC
Click here for the information on MDC Housing
Click here for Berlin tourist information
Click here and like us on Facebook
Click here for photos and datasets from the Analysis of Next Generation Sequence Data Mendelian Traits - Berlin: September 2015
Click here for photos and datasets from the Genetic Association Course - Berlin: June 2015
Click here for photos and datasets from the Analysis of Next Generation Sequence Data Complex Traits - Berlin: March 2015
Click here for photos and datasets from the Genetic Association Course - Berlin: June 2015
Click here for photos and datasets from the Complex Trait Analysis of NGS Data Course - Berlin: March 2015
Click here for photos and datasets from the Next Generation Sequence Data Analysis Course - Berlin: June 2014
Click here for photos and datasets from the Genetic Association Course - Berlin: March 2014
Click here for photos and datasets from the Genetic Association Course - Berlin: June 2013
Click here for photos and datasets from the Basic Gene Mapping Course - Berlin: November 2012
Click here for photos from the Genetic Association Course - Berlin: July 2012
Click here for photos from the Basic Gene Mapping Course - Berlin: November 2011
Click here for photos from the Genetic Association Course - Berlin: July 2011
Click here for photos from the Basic Gene Mapping Course - Berlin: October 2010
Click here for photos from the Genetic Association Course - Berlin: May 2010
Click here for photos from the Basic Gene Mapping Course - Berlin: November 2009
Click here for photos from the Basic Gene Mapping Course - Berlin: July 2008
Click here for photos from the Basic Gene Mapping Course - Berlin: July 2007
Click here for photos from the Basic Gene Mapping Course - Berlin: July 2006
Click here for photos from the Basic Gene Mapping Course - Berlin: July 2005
Click here for photos from the Basic Gene Mapping Course - Berlin: July 2004
Click here for photos from the Basic Gene Mapping Course - Berlin: July 2003

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