Changes
From Statistical Genetics Courses
/* Heather Cordell */
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[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===
* [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).
