Genotype Browser

GenotypeBrowser is a graphical user interface that allows users to browse FinnGen genotype data. The browser is available among FinnGen applications in the Sandbox and therefore requires red data access. The latest version of the GenotypeBrowser available in SandBox utilises R12 data.

In the GenotypeBrowser it is possible to:

• Get the number of genotypes for a variant of interest and to download a list of individuals carrying that variant to your working environment in SandBox. The result contains combined genotype, minimal phenotype and intensity data whenever available for the variant.

• Create cohorts based on genotype content and explore further phenotype content in CohortOperations, LifeTrack or other FinnGen tools.

• Perform quality control a SNP of interest through the interactively cluster plot visualisation tool.

• If a variant of interest is available in the imputation reference panel, it is possible to get the individuals with only imputed / directly genotyped calls.

• Get an overview on the geographical distribution of a variant.

• Get a source of genotype.

For the most complete documentation, please see the section Genotype Browser. This document provides background on the genotype browser that will help you interpret the options and results.

Tutorial

Genotype browser was also covered in tutorial form at Users' meeting:

FinnGen users’ meeting 9th February 2021.

Presentation

Presentation with use case examples Genotype browser menu options and FinnGen Users' Meeting 9th Feb 2021 recording at 19min 15sec and at 39min 05sec.