Changes
From Statistical Genetics Courses
/* Heather Cordell */
<!--[https://statgen.research.bcm.edu/files/2017/01/Rockefeller_advanced_course_flyer_2017.pdf Click here for course flyer] – Please Post and Distribute-->
[https://statgen.research.bcm.edu/files/2017/01/adv_gene_mapping_schedule_2017.pdf Click here for course schedule]
===Course Participants===
[[File:2017-01_Participants.jpg|none|427x200px]]
===Lecture Handouts & Practical Exercises===
====Gonçalo Abecasis====
* Presentations
** [https://statgen.research.bcm.edu/files/2017/01/abecasis/presentation/Genome-wide_Analysis.pdf Genome-wide Analysis]
** [https://statgen.research.bcm.edu/files/2017/01/abecasis/presentation/Genotype_Imputation.pdf Genotype Imputation]
** [https://statgen.research.bcm.edu/files/2017/01/abecasis/presentation/Meta_Analysis.pdf Meta Analysis]
** [https://statgen.research.bcm.edu/files/2017/01/abecasis/presentation/Sequence_Data.pdf Sequence Data]
====Heather Cordell====
* Presentations
** [https://statgen.research.bcm.edu/files/2017/01/cordell/hjc-NY2016-GWAS-nopage.pdf Statistical Methods]
** [https://statgen.research.bcm.edu/files/2017/01/cordell/HJC-interactions2017-nopage.pdf Interactions]
* Exercises
** [https://statgen.research.bcm.edu/files/2017/01/cordell/hjc-epistasis2015-ComputerPractical.pdf Interaction analysis using PLINK, CASSI, ORMDR and BEAM3]
** [https://statgen.research.bcm.edu/files/2017/01/cordell/cordell.tar.bz2 Download Data Sets] (decompress using "tar jxvf cordell.tar.bz2")
====Nancy Cox====
* [http://statgen.us/files/2017/01/cox/Cox_NewYork_talks.pdf Presentation]
* [http://statgen.us/files/2017/01/cox/ClassTutorial.docx Exercise]
====Suzanne Leal====
* Presentations
** [https://statgen.research.bcm.edu/files/2017/01/leal/presentation/data_quality_control_M2.pdf QC of Genotype Data]
** [https://statgen.research.bcm.edu/files/2017/01/leal/presentation/NGS%20Data%20Quality%20Control_M3.pdf QC of NGS Data]
** [https://statgen.research.bcm.edu/files/2017/01/leal/presentation/analysis_rare_variants_part_1.pdf Analysis of Rare Variant Data - Part 1]
** [https://statgen.research.bcm.edu/files/2017/01/leal/presentation/analysis_of_rare_variants_part_2.pdf Analysis of Rare Variant Data - Part 2]
** [https://statgen.research.bcm.edu/files/2017/01/leal/presentation/power_analysis_rare_variants_T2.pdf Power Analysis]
* Exercises
** [https://statgen.research.bcm.edu/files/2017/01/leal/docs/PLINK_data_QC_M1.pdf GWAS QC]
** [https://statgen.research.bcm.edu/files/2017/01/leal/docs/GWAS_Data_Controlling_for_Substructure_M2.pdf GWAS ASSOC MDS]
** [https://statgen.research.bcm.edu/files/2017/01/leal/docs/GenABEL-Rockefeller_M_3.pdf GenABEL]
** [https://statgen.research.bcm.edu/files/2017/01/leal/docs/22-1-VAT-JAN2016NYC_T1.pdf VAT]
** [https://statgen.research.bcm.edu/files/2017/01/leal/docs/Armitage_sample_size_NYC_2017_T_2.pdf Armitage Power]
** [https://statgen.research.bcm.edu/files/2017/01/leal/docs/22-3-SEQPower-JAN2016NYC_T3.pdf SEQPower]
** [https://statgen.research.bcm.edu/files/2017/01/leal/data/leal.tar.bz2 Download Data Sets] (decompress using "tar jxvf leal.tar.bz2")
** [https://statgen.research.bcm.edu/files/2017/01/leal/data/ExAC.DB.bz2 Download ExAC Database] (decompress using "bzip2 -d ExAC.DB.bz2")
* Commands
====Shamil Sunyaev====
* Presentations
** [http://statgen.us/files/2017/01/sunyaev/Rockefeller_complex_traits_2017_six_per_page.pdf Evolution, maintenance and allelic architecture of complex traits]
** [http://statgen.us/files/2017/01/sunyaev/Rockefeller_function_2017_six_per_page.pdf Annotating Gene Sequence Variation]
** [http://statgen.us/files/2017/01/sunyaev/Rockefeller_pop_gen_2017_six_per_page.pdf Population Genetics]
* Exercises
** [http://statgen.us/files/2017/01/sunyaev/Rockefeller_tutorial.pdf hypertriglyceridemia example]
** [http://genetics.bwh.harvard.edu/wiki/sunyaevlab/jlim Joint Likelihood Mapping]
** [http://genetics.bwh.harvard.edu/pines PINES]
===Software===
