Changes
From Statistical Genetics Courses
/* Heather Cordell */
For additional information on scientific program contact the course organizer Suzanne Leal:<br />email: [mailto:sleal@bcm.edu sleal@bcm.edu] or [mailto:suzannemleal@gmail.com suzannemleal@gmail.com]<br />Tel: +1 (713) 798-4011
<!--Application deadline is Friday, November 18, 2016--><!--[https://statgen.research.bcm.edu/files/2017/01/Application_Advanced_Gene_Mapping_Jan_2017.htm Click here for application form]--><!--[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/Application_Advanced_Gene_Mapping_Jan_2017abecasis/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.htm Click here for application formpdf Sequence Data]
====Heather Cordell====* Presentations** [https://statgen.research.bcm.edu/files/2017/01/Rockefeller_advanced_course_flyer_2017cordell/hjc-NY2016-GWAS-nopage.pdf Click here for course flyerStatistical Methods] – Please Post ** [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 DistributeBEAM3]** [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** [[AdvGeneMap2017Commands |GenABEL, GWAS and VAT 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===* [http://sites.stat.psu.edu/~yuzhang/ BEAM3]* [http://cassi.cas.org/ CASSI]* [http://cnsgenomics.com/software/gcta/mlmassoc.html GCTA-MLMA]* [http://www.genabel.org/ GenABEL]* [http://genome.sph.umich.edu/wiki/GotCloud GotCloud]* [https://cran.r-project.org/web/packages/ORMDR/index.html ORMDR]* [http://csg.sph.umich.edu/abecasis/MACH/ MACH]* [http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/ Matrix eQTL]* [http://csg.sph.umich.edu/abecasis/metal/ METAL]* [http://genome.sph.umich.edu/wiki/Minimac3 Minimac]* [http://pngu.mgh.harvard.edu/~purcell/plink/ PLINK]* [https://github.com/hakyimlab/PrediXcan PrediXCan]* [https://www.r-project.org/ R]* [http://genome.sph.umich.edu/wiki/RAREMETAL RareMetal]* [http://genome.sph.umich.edu/wiki/RAREMETALWORKER RareMetalWorker]* [http://www.bioinformatics.org/spower/ SEQPower]* [http://varianttools.sourceforge.net/Association/HomePage VAT] ===Links===* [http://ihg.helmholtz-muenchen.de/cgi-bin/hw/power2.pl Armitrage Test for Trends]* [http://agvgd.iarc.fr/ AlignGVGD]* [http://mendel.stanford.edu/SidowLab/downloads/gerp/index.html GERP]* [http://www.genmapp.org/ GenMAPP]* [http://mendel.stanford.edu/SidowLab/downloads/mapp/index.html MAPP]* [http://mips.helmholtz-muenchen.de/proj/ppi/ MIPS] .* [http://www.mutationtaster.org/ MutationTaster]* [http://mutpred.mutdb.org/ MutPred]* [http://www.rcsb.org/ PDB]* [http://pfam.sanger.ac.uk/ Pfam]* [http://genetics.bwh.harvard.edu/pph2 Polyphen-2]* [http://sift.jcvi.org/ SIFT]* [http://smart.embl.de/ SMART]* [http://www.rostlab.org/services/snap/ SNAP]* [http://snps3d.org/ SNPs3D]* [http://string.embl.de/ STRING]* [http://www.uniprot.org/ UniProt]
This course is supported by a grant from the National Institute of Health (NIH) - National Human Genome Research Institute (NHGRI).
