===More Information===
The maximum number of participants is 30. The course will take place in the Great Hall in Welch at The Rockefeller University, Students will perform exercises by connecting to the cloud using their own laptops. Laptops are also available for students to use for the duration of the course. The course is wheelchair accessible. All disabilities will be accommodated. Handicapped individuals are encouraged to apply.
Four travel stipends of up to $1,000 each are available. Eligibility requirements are: (1) sufficient background and practical experience in statistical analysis of genetic data, and (2) demonstrated financial need. Preference for stipends will be given to pre-doctoral students and postdoctoral researchers. To apply for such a stipend, please attach a letter of request and enclose a letter of reference and proof of student or postdoctoral status.
Tel: +1 (713) 798-4011
Application deadline is Monday, November 12, 2018
[httpshttp://statgen.research.bcm.eduus/files/2019/Application_Advanced_Gene_Mapping_Jan_2019Rockefeller_advanced_course_flyer_2019.html pdf Click here for application formcourse flyer]– Please Post and Distribute
[httpshttp://statgen.research.bcm.eduus/files/2019/Rockefeller_advanced_course_flyer_2019adv_gene_mapping_schedule_2019.pdf Click here for course flyerschedule] – Please Post and Distribute
===Lecture Handouts=======Gonçalo Abecasis====* Presentations** [httpshttp://statgen.researchus/files/2019/01/slides/abecasis/00.bcm%20Warm-up%20to%20Genomewide%20Analyses.edupdf Genome-wide Analysis]** [http://statgen.us/files/2019/adv_gene_mapping_schedule_201901/slides/abecasis/01.%20Genotype%20Imputation.pdf Click here Genotype Imputation]** [http://statgen.us/files/2019/01/slides/abecasis/02.%20Meta-Analysis.pdf Meta Analysis]** [http://statgen.us/files/2019/01/slides/abecasis/03.%20Sequencing.pdf Sequencing]<!--* Data Sets** [http://statgen.us/files/2018/01/abecasis/exercises.tar.gz Download]--> ====Heather Cordell====* Presentations** [http://statgen.us/files/2019/01/slides/cordell/hjc-NY2016-GWAS-nopage.pdf Genome-wide Association Studies - case/control and family-based]** [http://statgen.us/files/2019/01/slides/cordell/hjc-NY2019-MixedModels-nopage.pdf Mixed Models and Family-Based Methods]* Exercises** [http://statgen.us/files/2019/01/slides/cordell/Computer%20Practical%20Exercise.pdf Family-based Association Analysis - FaST-LMM, PLINK and R]** [http://statgen.us/files/2019/01/slides/cordell/Computer%20Practical%20Exercise%202.pdf Mixed models Association Analysis Computer - GCTA, PLINK, and R] ====Nancy Cox====* Presentations** [http://statgen.us/files/2019/01/slides/cox/DataIntegration_Cox_Lecture2_NJC_2019.pdf Data Integration] ====Suzanne Leal====* Presentations** [http://statgen.us/files/2019/01/slides/leal/data_quality_control_1.pdf Data Quality Control]** [http://statgen.us/files/2019/01/slides/leal/NGS_data_qc.pdf NGS Data Quality Control]** [http://statgen.us/files/2019/01/slides/leal/analysis_rare_variants.pdf Complex Trait Association Analysis of Rare Variants]** [http://statgen.us/files/2019/01/slides/leal/Trio_and_Family_Based_Association_analysis_3_new_format.pdf Family Based Rare Variant Association Analysis: Trios, Sibpairs and Extended Families]** [http://statgen.us/files/2019/01/slides/leal/power_sample_sizes.pdf Power Analysis for course scheduleIndividual Variants and Rare Variant Aggregate Association Analysis] ====Shamil Sunyaev====* Presentations** [http://statgen.us/files/2019/01/slides/sunyaev/Rockefeller_polygenic_2019.pdf Genetic Risk Prediction]** [http://statgen.us/files/2019/01/slides/sunyaev/Rockefeller_complex_traits_2019.pdf Evolution, maintenance and allelic architecture of complex traits]** [http://statgen.us/files/2019/01/slides/sunyaev/Rockefeller_function_2019.pdf Annotating gene sequence variation]** [http://statgen.us/files/2019/01/slides/sunyaev/Rockefeller_pop_gen_2019.pdf Intro to population genetics] ===Practical Exercises===* [http://statgen.us/files/2019/01/exercise_booklet_1_24_19.pdf Exercise Booklet] * [http://statgen.us/files/tutorials/gwas-qc/PLINK_data_QC_V2.pdf Genome-wide Association Analysis - Quality Control - PLINK]* [http://statgen.us/files/tutorials/gwas-substructure/GWAS_Data_Controlling_for_Substructure_V2.pdf Genome-wide Association Analysis - MDS and PCA – PLINK]* [http://statgen.us/files/tutorials/vat/VAT_exercise_2019_1_nographs.pdf Sequence data quality control and association analysis (VAT)]* [http://statgen.us/files/tutorials/pseq/PSEQ_exercise_2019.pdf Association Analysis of Sequence Data using PLINK/SEQ (PSEQ)]* [http://statgen.us/files/tutorials/rvtdt/rvtdt_exercise_v3.pdf Rare-Variant Transmission Disequilibrium Test (RV-TDT)]* [http://statgen.us/files/tutorials/Armitage_sample_size_revised.pdf Power and Sample Size Calculations – Cochran Armitage Test for Trend ]* [http://statgen.us/files/tutorials/functional-annotation/FunctionalAnnotation_exercise_2019.pdf Functional Annotation] * [http://csg.sph.umich.edu/abecasis/MaCH/tour/ MaCH]* [https://genome.sph.umich.edu/wiki/METAL_Quick_Start METAL]* [https://genome.sph.umich.edu/wiki/Tutorial:_RAREMETAL RAREMETAL] ===Exercise Data Sets===* [http://statgen.us/files/2019/01/datasets/Plink_DataQC.tar.gz Genome-wide Association Analysis - Quality Control - PLINK]* [http://statgen.us/files/2019/01/datasets/Plink_substructure.tar.gz Genome-wide Association Analysis - MDS and PCA – PLINK]* [http://statgen.us/files/2019/01/datasets/FASTLMMLGCTA.tar.gz Family-based Association Analysis- FaST-LMM, PLINK]* [http://statgen.us/files/2019/01/datasets/FASTLMMLGCTA.tar.gz Mixed models Association Analysis Computer – GCTA, PLINK and R]* [http://statgen.us/files/2019/01/datasets/Plink_DataQC.tar.gz Sequence data quality control and association analysis (VAT)]* [http://statgen.us/files/2019/01/datasets/pseq.tar.gz Association Analysis of Sequence Data using PLINK/SEQ (PSEQ)]* [http://statgen.us/files/2019/01/datasets/rvtdt.tar.gz Rare-Variant Transmission Disequilibrium Test (RV-TDT)]* [http://statgen.us/files/2019/01/datasets/FunctionalAnnotation.tar.gz Functional Annotation]* [http://statgen.us/files/2019/01/datasets/mach.tar.gz MaCH]* [http://statgen.us/files/2019/01/datasets/metal.tar.gz METAL]* [http://statgen.us/files/2019/01/datasets/raremetal.tar.gz RAREMETAL]
===Commands===
:::* [[Genome-wide Association-Quality Control Exercise|Genome-wide Association Analysis-Quality Control-PLINK]]* [[Genome-wide Association-MDS and PCA Exercise|Genome-wide Association Analysis-MDS and PCA-PLINK]]* [[Family-based Association Exercise|Family-based Association Analysis- FaST-LMM, PLINK and R]]:::* [[GATK_IGV_ExerciseMixed models Association Analysis_Exercise|GATK/IGVMixed models Association Analysis Computer – GCTA, PLINK and R]]:::* [[Popgen_ExerciseVAT_Exercise|PopgenSequence data quality control and association analysis (VAT)]]:::* [[PSEQ_Exercise|Association Analysis of Sequence Data using PLINK/SEQ (PSEQ)]]:::* [[Regression_ExerciseRV-TDT_Exercise|RegressionRare-Variant Transmission Disequilibrium Test (RV-TDT)]]:::* [[RV-TDT_ExerciseFunctional Annotation_Exercise|RV-TDTFunctional Annotation]] ===Software===* [http://www.openbioinformatics.org/annovar/ ANNOVAR]* [https://github.com/MicrosoftGenomics/FaST-LMM FasT-LLM]* [https://cnsgenomics.com/software/gcta/ GCTA]* [https://genome.sph.umich.edu/wiki/MaCH MaCH]* [SEQPower_Exercise|SEQPowerhttps://genome.sph.umich.edu/wiki/METAL METAL]* [https://genome.sph.umich.edu/wiki/Minimac Minimac]* [http://zzz.bwh.harvard.edu/plink/ PLINK]* [https://atgu.mgh.harvard.edu/plinkseq/ PLINK/SEQ]* [https://genome.sph.umich.edu/wiki/RAREMETAL RAREMETAL]* [[VAT_ExerciseRV-TDT|VATRV-TDT]]* [http://bioinformatics.org/spower/ SEQPower]* [http://varianttools.sourceforge.net/ Variant Association Tools]
This course is supported by a grant from the National Institute of Health (NIH) - National Human Genome Research Institute (NHGRI).