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  • H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 1

    20 August 2018

    H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 1 https://tess.elixir-europe.org/events/h3abionet-2018-genotyping-chip-data-analysis-and-gwas-lecture-series #### Computational requirements for running the H3ABioNet GWAS workflows The first of a series of seven online lectures for Genome Wide Association Studies (GWAS) will cover the technical requirements for setting up a your computational environment for running the H3ABioNet GWAS workflows. In this inaugural lecture of the series, Prof. Hazelhurst will cover the the following topics: Installing and using Nextflow Installing and using Github Use of containers for packaging and running tools Pulling the GWAS pipeline from Github and running it As this lecture aims to provide attendees with an environment to the run the H3ABioNet GWAS workflow at their own pace, there are some preliminary software requirements: Either a Linux machine or an Apple running macOS Ideally you should have machine with at least 2-4 cores and 8GB of RAM. Java 8 Nextflow installed (see installation instructions at https://www.nextflow.io/) Python 3 Please also install either Docker OR the following dependencies using pip3: Pandas, Matplotlib, Openpyxl, SciPy, NumPy PLINK 1.9 [Please also refer to the following documentation to obtain the H3ABioNet GWAS workflow]: https://github.com/h3abionet/h3agwas/blob/master/README.md 2018-08-20 15:00:00 UTC 2018-08-20 16:30:00 UTC H3ABioNet Population genomics Genotyping experiment Computational biology Workflows GWAS study Bioinformatics H3ABioNet info@h3abionet.org H3ABioNet Anyone intersted in GWAS and using the H3Africa genotyping chipAnyone who wants to learn more about GWAS workshops_and_courses [] NextflowDockerH3ABioNetGWASWorkflowsGenotyping array analysis bioinformaticsAfricaPopulation GenomicsReproducible ScienceH3Africa genotyping arrayHigh performance computingCloud computingGWAS workflowH3ABioNet GWAS 2018 Lecture Series
  • H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 5

    3 September 2018

    H3ABioNet 2018 Genotyping Chip Data Analysis and GWAS lecture series - Lecture 5 https://tess.elixir-europe.org/events/h3abionet-2018-genotyping-chip-data-analysis-and-gwas-lecture-series-ce96b48a-423a-435c-beae-9ddfcaba38a6 ### Population structure in GWAS The fifth of a series of seven H3ABioNet online lectures for Genome Wide Association Studies (GWAS) will introduce the concept of population structure/stratification (PS) and suggest why it is critical to consider PS in a GWAS. The lecture will begin by familiarizing the types of PS that are encountered and explain the factors that could cause them to appear in a GWAS dataset. It will then cover the methods that are commonly used to identify PS in a dataset and finally discuss the available computational approaches to correct for PS in a GWAS. Date: 3rd September 2018 Time: 2pm WAT / 3pm CAT / 4pm EAT [Url to join the lecture]: http://meeting.uct.ac.za/h3abionet_gwas/ 2018-09-03 15:00:00 UTC 2018-09-03 16:30:00 UTC H3ABioNet Genotyping experiment Bioinformatics GWAS study Population genetics Population genomics H3ABioNet info@h3abionet.org H3ABioNet Anyone intersted in GWAS and using the H3Africa genotyping chip 150 meetings_and_conferencesworkshops_and_courses first_come_first_served Population structureGWASCorrect for population structureH3ABioNetH3AfricaAWI-GEN
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