Difference between revisions of "2015AdvancedGeneMapping"
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====Ben Neale==== | ====Ben Neale==== | ||
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| − | * [http://statgen.us/files/2015/02/neale/handouts/Neale_Rockefeller_course_2015.pdf Neale lectures combined] | + | ** [http://statgen.us/files/2015/02/neale/handouts/Neale_Rockefeller_course_2015.pdf Neale lectures combined] |
* Exercises | * Exercises | ||
** [http://statgen.us/files/2015/02/neale/exercises/neale.tar.bz2 Download Data Sets] (decompress using "tar jxvf neale.tar.bz2") | ** [http://statgen.us/files/2015/02/neale/exercises/neale.tar.bz2 Download Data Sets] (decompress using "tar jxvf neale.tar.bz2") | ||
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====Shamil Sunyaev==== | ====Shamil Sunyaev==== | ||
* Presentations | * Presentations | ||
| − | ** [http://statgen.us/files/ | + | ** [http://statgen.us/files/2015/02/sunyaev/handouts/Rockefeller_pop_gen_2014.pdf Population genetics] |
| − | ** [http://statgen.us/files/ | + | ** [http://statgen.us/files/2015/02/sunyaev/handouts/Rockefeller_mutation_2015.pdf Mutation] |
| − | ** [http://statgen.us/files/ | + | ** [http://statgen.us/files/2015/02/sunyaev/handouts/Rockefeller_complex_traits_2015.pdf Complex traits] |
* Exercises | * Exercises | ||
| − | ** [http://statgen.us/files/ | + | ** [http://statgen.us/files/2015/02/sunyaev/handouts/Rockefeller_tutorial.pdf Annotation tutorial] |
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===Data-sets Used During the Course=== | ===Data-sets Used During the Course=== | ||
| − | * [http://statgen.us/files/ | + | * [http://statgen.us/files/2015/02/cordell/exercises/cordell.tar.bz2 Heather Cordell's Data Sets] |
| − | * [http://statgen.us/files/ | + | * [http://statgen.us/files/2015/02/francioli/exercises/francioli.tar.bz2 Laurent Francioli's Data Sets] |
| − | * [http://statgen.us/files/ | + | * [http://statgen.us/files/2015/02/leal/exercises/leal.tar.bz2 Suzanne Leal's Data Sets] |
| − | * [http://statgen.us/files/ | + | * [http://statgen.us/files/2015/02/neale/exercises/neale.tar.bz2 Ben Neale's Data Sets] |
In order to obtain a particular data set, please follow the following steps: | In order to obtain a particular data set, please follow the following steps: | ||
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# Change to this subdirectory (''cd'' command) and proceed with the exercise. | # Change to this subdirectory (''cd'' command) and proceed with the exercise. | ||
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===Software=== | ===Software=== | ||
* [http://annovar.openbioinformatics.org/en/latest/ ANNOVAR] | * [http://annovar.openbioinformatics.org/en/latest/ ANNOVAR] | ||
Latest revision as of 15:09, 7 June 2016
Contents
Advanced Gene Mapping Course
The Rockefeller University, New York, Monday through Friday, Feb. 9-13, 2015
General Information
The course emphasis is analysis of complex human disease traits; concentrating on methods to detect rare and common variant associations. The course includes theory as well as practical exercises.
Topics include: Analysis of whole genome association studies; analysis of rare variants using next generation sequence and exome chip data; rare variant association tests; analysis of qualitative and quantitative traits (population and family-based data); detection of de novo variants and significance testing; Mendelian randomization; determining whether inflated test statistics observed with large scale GWAS meta-analysis is driven by confounding or by polygenic inheritance using the LD score approached; functional predication of variant sites; variant annotation, sequence read alignment and variant calling, controlling for population substructure/admixture (principal components analysis/multidimensionality scaling); data quality control of genotype and sequence data; detection of gene x gene interaction; sample size estimation and evaluating power for common and rare variants.
The exercises will be carried out using a variety of computer programs including ANNOVAR, GATK,GenAbel, GERP, PLINK, R, SIFT, SEQPower, Variant Association Tools (VAT), Polyphen-2, etc.
Course Instructors
The instructors for the course are: Heather Cordell (University of Newcastle), Laurent Francioli (University Medical Center Utrecht), Suzanne Leal (The Rockefeller University & Baylor College of Medicine), Ben Neale (Broad Institute and Harvard University) and Shamil Sunyaev (Harvard University).
Lecture Handouts & Practical Exercises
Heather Cordell
- Presentations
- Exercises
- Interaction analysis
- Download Data Sets (decompress using "tar jxvf cordell.tar.bz2")
Laurent Francioli
- Presentations
- Exercises
- Variant calling exercises
- Download Data Sets (decompress using "tar jxvf francioli.tar.bz2")
Suzanne Leal
- Presentations
- Exercises
Ben Neale
- Presentations
- Exercises
- Download Data Sets (decompress using "tar jxvf neale.tar.bz2")
Shamil Sunyaev
- Presentations
- Exercises
Software
Links
- Armitrage Test for Trends
- AlignGVGD
- GERP
- GenMAPP
- MAPP
- MIPS .
- MutationTaster
- MutPred
- PDB
- Pfam
- Polyphen-2
- SIFT
- SMART
- SNAP
- SNPs3D
- STRING
- UniProt
This course is supported by a grant from the National Institute of Health (NIH) - National Human Genome Research Institute (NHGRI).
