Changes

[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

[https://statgen.research.bcm.edu/files/2019/adv_gene_mapping_schedule_2019.pdf Click here for course schedule] ===Lecture Handouts & Practical Exercises===

** [httpshttp://statgen.research.bcm.eduus/files/2018/01/abecasis/exercises.tar.gz Download]

** [httpshttp://statgen.research.bcm.eduus/files/2019/01/slides/cordell/hjc-NY2016-GWAS-nopage.pdf Genome-wide association studies (Association Studies - case/control and family-based)]** [httpshttp://statgen.research.bcm.eduus/files/2019/01/slides/cordell/hjc-NY2019-MixedModels-nopage.pdf Mixed Models and familyFamily-based methods for genetic association analysisBased Methods]

** [httpshttp://statgen.research.bcm.eduus/files/2019/01/slides/cordell/Computer%20Practical%20Exercise.pdf Family-based Association using Analysis - FaST-LMM, PLINK and R]** [httpshttp://statgen.research.bcm.eduus/files/2019/01/slides/cordell/Computer%20Practical%20Exercise%202.pdf Mixed models Association Analysis Computer - GCTA, PLINK, and R]

** [httpshttp://statgen.research.bcm.eduus/files/20182019/01/cox/GeneticArchitecture_Transcriptomics_Cox_2018.pdf Integrative Approaches for Genetic Studies of Common Human Disease - Genetic Architecture andTranscriptomics]** [https://statgen.research.bcm.edu/files/2018/01slides/cox/DataIntegration_Cox_2018DataIntegration_Cox_Lecture2_NJC_2019.pdf Integrative Approaches for Genetic Studies of Common Human Disease - Data Integration: Genome x Transcriptome x EHR]-->

** [httpshttp://statgen.research.bcm.eduus/files/20182019/01/leal/Analysis_rare_variants_3.pdf Complex Trait Association Analysis of Rare Variants Obtained from Sequence Data: Population-Based Data]** [https://statgen.research.bcm.edu/files/2018/01slides/leal/data_quality_control_1.pdf Data Quality Control]** [httpshttp://statgen.research.bcm.eduus/files/20182019/01/leal/Trio_and_Family_Based_Association_analysis_4.pdf Family Base Association Analysis]** [https://statgen.research.bcm.edu/files/2018/01slides/leal/NGS_variant_calling_QC_2NGS_data_qc.pdf NGS Data Quality Control]** [httpshttp://statgen.research.bcm.eduus/files/20182019/01/leal/SEQSpark_5.pdf SEQSpark]* Exercises** [https://statgen.research.bcm.edu/files/2018/01slides/leal/PLINK_data_QC_V2_1analysis_rare_variants.pdf PLINK GWAS Data QC]** [https://statgen.research.bcm.edu/files/2018/01/leal/GWAS_Data_Controlling_for_Substructure_V2_2.pdf PLINK GWAS Complex Trait Association Analysis Controlling for Population Substructureof Rare Variants]** [httpshttp://statgen.research.bcm.eduus/files/20182019/01/leal/GenABEL_with_PLINK1.9_3.pdf GenABEL]** [https://statgen.research.bcm.edu/files/2018/01slides/leal/rvtdt_exercise_v2Trio_and_Family_Based_Association_analysis_3_new_format.pdf RV-TDT]** [httpsFamily Based Rare Variant Association Analysis://statgen.research.bcm.edu/files/2018/01/leal/FunctionalAnnotation_exercise_2018v2.pdf Functional AnnotationTrios, Sibpairs and Extended Families]** [httpshttp://statgen.research.bcm.eduus/files/20182019/01/leal/SEQSpark_exercise_Final_v1.pdf SEQSpark]** [https://statgen.research.bcm.edu/files/2018/01slides/leal/VAT_exercise_revised_nographspower_sample_sizes.pdf VAT]* Commands** [[AdvGeneMap2018Commands|Exercise Commands]]* Exercise Datasets** [https://statgen.research.bcm.edu/files/2018/01/leal/exercises.tar.gz DownloadPower Analysis for Individual Variants and Rare Variant Aggregate Association Analysis]-->

** [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]

:::* [[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)]]:::* [[Functional Annotation_Exercise|Functional Annotation]]