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Common & rare association
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A1. Introduction to common variation - Part 1
LucÃa Colodro-Conde, June 2021 Virtual Workshop
This video introduces some fundamental terms and concepts, including types of genetic variation and allele frequency.
A2. Introduction to common variation - Part 2
LucÃa Colodro-Conde, June 2021 Virtual Workshop
This video introduces reference panels, linkage disequilibrium, differences across ancestry, the genome browser, and genomic assembly (or build).
B01. Why is qualtiy control important?
Katrina Grasby, June 2021 Virtual Workshop
A brief description of how genotyped data is generated from DNA and the steps to clean and check genotyped data prior to imputation and/or using it in analyses.Ìý
B02. PLINK 101: What is PLINK and how do we use it?
LucÃa Colodro-Conde, June 2021 Virtual Workshop
An introduction to PLINK file formats, using the command line, and websites.
B03. PLINK 101: Using PLINK for quality control (Practical)
LucÃa Colodro-Conde & Katrina Grasby, June 2021 Virtual Workshop
These are the files used in the practical held during the 2021 virtual workshop.
B04. Introduction to GWAS - Part 1
Katrina Grasby, June 2021 Virtual Workshop
A basic introduction to GWAS and the commonly used regression models.
B05. Introduction to GWAS - Part 2
Katrina Grasby, June 2021 Virtual Workshop
This introduces ideas of population stratification as a confounder, the large multiple testing burden in GWAS, the challenge of power, and the need for replication.
B06. How and why do we impute SNP data?
Sarah Medland, June 2021 Virtual Workshop
This video talks about the concepts involved in imputation of SNP data using public reference panels.
B07. Running GWAS with generalized mixed models
Wei Zhou, June 2021 Virtual Workshop
This is a lecture to introduce the R package SAIGE, which was developed for conducting GWASs in large-scale biobanks, while accounting for unbalanced case-control ratios, handling sample relatedness, and being scalable for large data sets.Ìý
B08. Running GWAS with biobank scale samples
Rounak Dey, June 2021 Virtual Workshop
This is a lecture about using the Saddlepoint approximation in Biobank-based PheWAS to account for unbalanced case-control ratios for binary phenotypes, which has been implemented in the R library SPAtest.
B09. How do we use meta-analysis in GWAS?
Sarah Medland, June 2021 Virtual Workshop
This video talks about the common methods used to conduct a GWAS meta-analysis and the software that is commonly used to do this.
B10. METAL 101: Meta-analysis Practical
Adrian Campos, June 2021 Virtual Workshop
This practical will show you how to run a GWAS meta-analyses.
C1. Introduction to sequencing
Kumar Veerapen, June 2021 Virtual Workshop
This video discusses traditional sequencing techniques.
C2. Evolution of sequencing
Kumar Veerapen, June 2021 Virtual Workshop
This video discusses the evolution of sequencing techniques and the scope of the data that the different types can generate.
C3. Next-gen sequencing informatics
Kumar Veerapen, June 2021 Virtual Workshop
This video discusses the initial bioinformatic analyses of next-gen sequencing data.
C4. Introduction to rare variant association using SKAT
Zhangchen Zhao, June 2021 Virtual Workshop
This is a lecture about set-based association tests for testing the association between rare genetic variants and human diseases and traits. It introduces the function called SKATbinary implemented in the SKAT library that conducts set-based association tests while accounting for unbalanced case-control ratios for binary phenotypes.Ìý
C5. Rare variant association tests in large-scale biobanks and cohorts
Wei Zhou, June 2021 Virtual Workshop
This is a lecture about conducting set-based association tests in large-scale biobanks and cohorts. It introduces the R package SAIGE-GENE, which was developed for conducting exome-wide or genome-wide set-based tests for rare variants in large-scale biobanks, while accounting for unbalanced case-control ratios, handling sample relatedness, and being scalable for large data sets.
C6. HAIL 101: Introduction to HAIL
Kumar Veerapen, June 2021 Virtual Workshop
The video explains what HAIL is and how and why you might want to use it.
C7. HAIL 101: Using HAIL on the cloud
Kumar Veerapen, June 2021 Virtual Workshop
This video discusses using cloud based computing for analysis of sequence data.
C8. HAIL 101: HAIL Practical
Kumar Veerapen, June 2021 Virtual Workshop
This practical walks you through some basic uses of HAIL.