Changes
From Statistical Genetics Courses
/* Handouts */
For additional information on scientific program contact the course organizer [mailto:suzannemleal@gmail.com?subject=Rockefeller Advanced Gene Mapping Course 2020 Suzanne Leal]: <br />email: [mailto:suzannemleal@gmail.com suzannemleal@gmail.com] or [mailto:sml3@cumc.columbia.edu sml3@cumc.columbia.edu] <br />Tel: +1 (212) 304-7047
==Course Photo==
[[File:142FBA93-B26F-45A4-A0C5-264B812AB558.JPG|thumb|none|]]
==Handouts======[//www.statgen.us/files/2020/01/Rockefeller_advanced_course_flyer_2020docs/lectures/Lecture_booklet.pdf All Lectures]========[//www.statgen.us/files/2020/01/docs/exercises/Booklet_exercises.pdf All Exercises]=======Heather Cordell=======Lectures====* [//www.statgen.us/files/2020/01/docs/lectures/NY2020-lecture1-nopause_4.pdf Genome-wide association studies (GWAS) - Part 1]* [//www.statgen.us/files/2020/01/docs/lectures/NY2020-lecture2-nopause_4.pdf Click here for course flyerGenome-wide association studies (GWAS) - Part 2] – Please Post and Distribute
====Exercises====* [[Tutorials#FastLMM | Family-based Association using FaST-LMM, PLINK and R]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/fastlmm-gcta.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta/tags docker image]* [[Tutorials#GCTA|GCTA]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/fastlmm-gcta.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/fastlmm-gcta/tags docker image]* [[Tutorials#Epistasis_.28PLINK_and_CASSI.29 | Interaction analysis using PLINK and CASSI]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/epistasis.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/epistasis/tags docker image] ===Nancy Cox=======Lectures====* [//www.statgen.us/files/2020/01/adv_gene_mapping_schedule_2020docs/lectures/LealCourse_Cox_Jan2020.pdf Click here for course scheduleIntegrative Approaches in Biobanks: Getting to Biological Mechanisms of Disease] ===Andrew DeWan=======Lectures====* [//www.statgen.us/files/2020/01/docs/lectures/Rockefeller_Adv_Course_DeWan_pleiotropy_4.pdf From cross-phenotype associations to pleiotropy in human genetic studies] ====Exercises====* [[Tutorials#Pleiotropy|Pleiotropy]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/pleiotropy.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/pleiotropy/tags docker image]
===Suzanne Leal===
====Lectures====
* [//www.statgen.us/files/2020/01/docs/lectures/data_quality_control_1.pdf Data Quality Control]
* [//www.statgen.us/files/2020/01/docs/lectures/NGS_data_qc.pdf NGS Data Quality Control]
* [//www.statgen.us/files/2020/01/docs/lectures/analysis_rare_variants_part_1.pdf Complex Trait Association Analysis of Rare Variants]
* [//www.statgen.us/files/2020/01/docs/lectures/power_sample_sizes.pdf Power Analysis for Single and Rare Variant Aggregate Association Analyses]
* [//www.statgen.us/files/2020/01/docs/lectures/Analysis_rare_variants_part_2.pdf National Heart Lung and Blood Institute Exome Sequencing Project]
====Exercises====
* [[Tutorials#PSEQ|PLINK/SEQ (PSEQ)]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/pseq.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/pseq/tags docker image]
* [[Tutorials#Variant_Association_Tools|Association Analysis of Sequence Data using Variant Association Tools for Complex Traits]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/vat.dockerfile dockerfile] and [https://hub.docker.com/r/statisticalgenetics/vat/tags docker image]
* [[Tutorials#Cochran_Armitage_Trend_Test|Cochran Armitage Trend Test for GWAS power analysis]]
* [[Tutorials#Annotation|ANNOVAR Annotation]] | [https://github.com/statgenetics/statgen-courses/blob/master/docker/annovar.dockerfile dockefile] and [https://hub.docker.com/r/statisticalgenetics/annovar/tags docker image]
===Bogdan Pasanuic===
====Lectures====
* [//www.statgen.us/files/2020/01/docs/lectures/finemapping_pasaniuc.pdf Statistical fine-mapping of GWAS signals]
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====Exercises====
* finemap
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===Shamil Sunyaev===
====Lectures====
* [//www.statgen.us/files/2020/01/docs/lectures/Rockefeller_pop_gen_2020.pdf Population Genetics]
* [//www.statgen.us/files/2020/01/docs/lectures/Rockefeller_complex_traits_2020.pdf Evolution, maintenance and allelic architecture of complex traits]
* [//www.statgen.us/files/2020/01/docs/lectures/Rockefeller_polygenic_2020.pdf Polygenic Risk Score]
* [//www.statgen.us/files/2020/01/docs/lectures/Rockefeller_function_2019.pdf Functional Annotation]
====Exercises====
* [Pleiotropy Exercise http[Tutorials#Polygenic_risk_prediction_.28NPS_method.29|Polygenic risk prediction using non-parametric shrinkage]] | [https://wwwgithub.statgen.uscom/filesstatgenetics/2020statgen-courses/01blob/docsmaster/exercisesdocker/pleio_exercisenps.docxdockerfile dockefile]* and [Pleiotropy Exercise Answers httphttps://wwwhub.statgendocker.uscom/filesr/2020statisticalgenetics/01nps/docs/exercises/pleio_exercise_answers.docxtags docker image]
This course is supported by a grant from the National Institute of Health (NIH) - National Human Genome Research Institute (NHGRI).
