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===Lecture Handouts=======Gon&ccedil;alo 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 for course scheduleGenotype 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]-->

===Commands=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 Association Exercise|Based Methods]* Exercises** [http://statgen.us/files/2019/01/slides/cordell/Computer%20Practical%20Exercise.pdf Family-based Association Analysis- FaST-LMM, PLINK and R]]:::** [[Mixed models Association Analysis_Exercise|http://statgen.us/files/2019/01/slides/cordell/Computer%20Practical%20Exercise%202.pdf Mixed models Association Analysis Computer – - GCTA, PLINK , and R]]:::* [[VAT_Exercise|Sequence data quality control and association analysis (VAT)]]:::* [[PSEQ_Exercise|Association Analysis of Sequence Data using PLINK/SEQ (PSEQ)]]:::* [[RV-TDT_Exercise|Rare-Variant Transmission Disequilibrium Test (RV-TDT)]]:::* [[Popgen_Exercise|Popgen]]:::* [[Regression_Exercise|Regression]]

====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 Individual 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]]* [[Mixed models Association Analysis_Exercise|Mixed models Association Analysis Computer – GCTA, PLINK and R]]* [[VAT_Exercise|Sequence data quality control and association analysis (VAT)]]* [[PSEQ_Exercise|Association Analysis of Sequence Data using PLINK/SEQ (PSEQ)]]* [[RV-TDT_Exercise|Rare-Variant Transmission Disequilibrium Test (RV-TDT)]]* [[SEQPower_ExerciseFunctional Annotation_Exercise|SEQPowerFunctional Annotation]]