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General Genetic Association Analysis Workflow

2.1 General Genetic Association Analysis Workflow

There is a myriad of approaches to genetic association analysis. Which steps you perform and when depends largely on the type of study you’re conducting (e.g. population vs. family), the types of variables you are analyzing (e.g. SNPs vs. CNVs), the scale of your study (e.g. candidate gene vs. whole genome), and the scientific questions you hope to answer. Outlined below is a general workflow for genetic association analysis using the SVS.

Create a new project
Create a new project.

Import data
Import genetic, phenotype, pedigree (if doing family analysis), and any other variables into your project.

Prepare data for analysis
Perform any necessary quality control, transformations, recoding, filtering, and principal component analysis on your data and then combine all “cleaned” data into a single spreadsheet.

Import and apply genetic marker map
Import a genetic marker map corresponding to the type of genetic data you are working with and apply it to the combined spreadsheet containing genetic data.

Perform association analysis
Perform the appropriate association test(s) corresponding to your data and study type.

Visualize results
Generate a series of plots to visualize your results.