=Complex Trait Analysis of Next Generation Sequence Data=
===March 6-10, 2017<br data-attributes="%20/">, Max Delbrück Center (MDC) for Molecular Medicine<br data-attributes="%20/">, Berlin, Germany===The third annual course on Complex Trait Analysis of Next Generation Sequence Data will be held at the MDC in Berlin from March 6-10, 2017. 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-, trio- and family-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.
The instructors for the course are ===Course Participants===[https[File://www.bcm.edu/research/labs/center2017-for03-statistical-genetics/ Suzanne Leal] (Baylor College of Medicine) and [http://portalParticipants.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/ Michael Nothnageljpg|none|500x375px]] (University of Cologne).
===General Information===
<!--The third annual course on Complex Trait Analysis of Next Generation Sequence Data will be held at the MDC in Berlin from March 6-10, 2017.-->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-, trio- and family-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 complex traits and evaluating variant functionality.
=====[http://statgen.us/files/2015/09/BerlinHotelTaxExemptionForm.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
[[File:MDC_C.jpg|none|250x250px]]
The building is red and stands across the street from the campus bus stop and the blue bear.
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.
For additional information on the course please contact [mailto:sleal@bcm.edu?subject=Genetic%20Association%20Course%2C%20Berlin%202015 Suzanne Leal]:
<!--Application Deadline January 5, 2017-->
:
:* email: [mailto:sleal@bcm.edu;suzannemleal@gmail.com?subject=Genetic%20Association%20Course%20Berlin%202016 sleal@bcm.edu]
:* Tel: +1 (713) 798-4011
:* Fax: +1 (713) 798-4012
===Instructors===
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).
[[File:2017-03-Instructors.jpg|none|250x333px]]
For additional information on ===[http://statgen.us/files/2017/03/auth/coursebook_lectures.pdf Course Slides]======Data-sets Used During the course please contact Course===:::* [mailtohttp:sleal@//statgen.us/files/2016/07/annotation.tar.bz2 Annotation exercise]:::* [http://statgen.us/files/2016/07/gatk.tar.bz2 GATK/IGV exercise]:::* [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/regression.tar.bz2 Regression exercise]:::* [https://statgen.research.bcm.edu?subject/files/2016/09/exercises/rvtdt.tar.gz RV-TDT exercise]:::* [http://statgen.us/files/2016/07/seqpower.tar.bz2 SEQPower exercise]:::* [http://statgen.us/files/2016/07/vat.tar.bz2 Variant Association Tools exercise] : =Genetic%20Association%20Course%2C%20Berlin%202015 Suzanne Leal==Commands===:::* [[Annotation_Exercise|Annotation]]:::* [[GATK_IGV_Exercise|GATK/IGV]]:::* [[Popgen_Exercise|Popgen]]:::* [[PSEQ_Exercise|PSEQ]]:::* [[Regression_Exercise|Regression]]:::* [[RV-TDT_Exercise|RV-TDT]]:::* [[SEQPower_Exercise|SEQPower]]:::* [[VAT_Exercise|VAT]] : ===Result Files===:::* [http://statgen.us/files/2016/07/gatk_results.tar.gz GATK/IGV exercise]
Application Deadline January 5, 2017: ===Software Links===:::* [https://www.broadinstitute.org/gatk/ GATK]:::* [http://www.broadinstitute.org/igv/ IGV] ([http://statgen.us/files/software/igv.jar Download JAR file]):::* [https://atgu.mgh.harvard.edu/plinkseq/ PSEQ]:::* [https://www.r-project.org/ R]:::* [http://bioinformatics.org/rv-tdt/ RV-TDT]:::* [http://www.bioinformatics.org/spower/start SEQPower]:::* [http://varianttools.sf.net/VAT Variant Association Tools]
: ===Bioinformatic Tools===:::* email[http: //cadd.gs.washington.edu/score CADD]:::* [mailtohttp:sleal@bcm//fathmm.biocompute.org.uk/inherited.html FATHMM]:::* [http://mendel.stanford.edu;suzannemleal@gmail/SidowLab/downloads/gerp/ GERP]:::* [http://www.com?subject=Genetic%20Association%20Course%20Berlin%202016 sleal@bcmgenetics.wustl.edu/jflab/lrt_query.html LRT]:::* Tel[http: +1 (713) 798//www.mutationtaster.org/ChrPos.html Mutation Taster]:::* [http://genome.ucsc.edu/cgi-4011bin/hgGateway Nucleotide Conservation]:::* Fax[http: +1 (713) 798//compgen.bscb.cornell.edu/phast/ PhyloP]:::* [http://genetics.bwh.harvard.edu/pph2/bgi.shtml PolyPhen-40122]:::* [http://provean.jcvi.org/genome_submit_2.php?species=human PROVEAN and SIFT]:::* [http://grch37.ensembl.org/Homo_sapiens/Tools/VEP VEP]
<!--: [https://statgen.research.bcm.edu/files/20162017/0703/schedule_berlin_complex_ngs_2016schedule_berlin_complex_ngs_2017.pdf Click here for course schedule]
[https://statgen.research.bcm.edu/files/20162017/0703/Berlin_NGS_Complex_Trait_Application_2016Berlin_NGS_Complex_Trait_Application_2017.html htm Click here for the application form]
[https://statgen.research.bcm.edu/files/20162017/0703/Berlin_NGS_complex_traits_course_flyer_2016Berlin_NGS_complex_traits_course_flyer_2017.pdf Click here for course flyer] (please post and distribute)
-->
[https://www.mdc-berlin.de/directions Click here for maps and directions to the MDC]<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/">
[https://www.facebook.com/statgencourses/?ref=aymt_homepage_panel Click here and like us on Facebook]<br />[https://statgen.research.bcm.edu/index.php/Genassoc2016 Click here for photos and datasets for data from Genetic Association Course – Berlin: September 2016]<br data-attributes="%20/">[https://statgen.research.bcm.edu/index.php/ComplexNGS2016 Click here for photos and datasets for the from Analysis of Complex of Next Generation Sequence Data for Complex Traits Course – Berlin: July 2016]<br data-attributes="%20/">[https://statgen.research.bcm.edu/2015SeptMDCindex.php/view 2015SeptMDC Click here for photos and datasets from the Analysis of Next Generation Sequence Data Mendelian Traits - Berlin: September 2015]<br data-attributes="%20/">[https://statgen.research.bcm.edu/2015JuneMDCindex.php/view 2015JuneMDC Click here for photos and datasets from the Genetic Association Course - Berlin: June 2015]<br data-attributes="%20/">[https://statgen.research.bcm.edu/2015MarchMDCindex.php/view 2015MarchMDC Click here for photos and datasets from the Analysis of Next Generation Sequence Data Complex Traits - Berlin: March 2015]<br data/>[http://portal.ccg.uni-attributeskoeln.de/ccg/index.php?id="%2089 Click here for photos and datasets from the Genetic Association Course - Berlin: June 2015]<br /">[http://portal.ccg.uni-koeln.de/ccg/researchindex.php?id=88 Click here for photos and datasets from the Complex Trait Analysis of NGS Data Course - Berlin: March 2015]<br /stat>[http://portal.ccg.uni-gen-bioinformaticskoeln.de/coursesccg/ngsdac2014index.html php?id=87 Click here for photos and datasets from the Next Generation Sequence Data Analysis Course - Berlin: June 2014]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2014index.html php?id=86 Click here for photos and datasets from the Genetic Association Course - Berlin: March 2014]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2013index.html php?id=85 Click here for photos and datasets from the Genetic Association Course - Berlin: June 2013]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2012index.html php?id=84 Click here for photos and datasets from the Basic Gene Mapping Course - Berlin: November 2012]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2012index.html php?id=83 Click here for photos from the Genetic Association Course - Berlin: July 2012]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2011index.html php?id=81 Click here for photos from the Basic Gene Mapping Course - Berlin: November 2011]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2011index.html php?id=80 Click here for photos from the Genetic Association Course - Berlin: July 2011]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2010index.html php?id=63 Click here for photos from the Basic Gene Mapping Course - Berlin: October 2010]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gac2010index.html php?id=62 Click here for photos from the Genetic Association Course - Berlin: May 2010]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2009index.html php?id=90 Click here for photos from the Basic Gene Mapping Course - Berlin: November 2009]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2008index.html php?id=91 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2008]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2007index.html php?id=92 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2007]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2006index.html php?id=93 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2006]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2005index.html php?id=94 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2005]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2004index.html php?id=95 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2004]<br data-attributes="%20/">[http://portal.ccg.uni-koeln.de/ccg/research/stat-gen-bioinformatics/courses/gmc2003index.html php?id=96 Click here for photos from the Basic Gene Mapping Course - Berlin: July 2003]