Imputation workshop

This in-person workshop is jointly hosted by LIC, Genomics Aotearoa and NeSI, and will be held on July 7th, 2023 from 9am to 5pm. The workshop will be held at the LIC premises in Hamilton. This workshop is for New Zealand scientists and will explore genotype imputation techniques.

Genotype imputation is a cost-efficient approach to approximate high-density genotypes or full sequence data from low-density genotypes/low-pass sequencing data of individuals. This workshop is intended for anyone interested in learning how to use either Beagle or Minimac to impute genotypes and how to evaluate the imputation performance of these methods.

This workshop will involve:

- A brief overview of imputation.

- Quality control and preparation of genetic data for imputation.

- Evaluation the imputation performance using different parameters.

Workshop attendees will observe demonstrations and then work through exercises.

Prerequisites

Attendees are expected to have some familiarity with basic bash and R. If you would like a refresher, you can find a copy of past workshops which cover the fundamentals of bash (here) and R (here). Additionally, to get the most out of this workshop it is encourage that attendees know about basic genetics and genomics.

Setup

This is a hands-on workshop. The workshop material will be run on the NeSI High Performance Computing (HPC) platforms - there is no need to install any software for this workshop. Instructions on how to access the NeSI HPC service will be sent out with the confirmation letter to registrants.

Participants must have their own machine to work on and plan to participate actively in the workshop. You will require a working web browser.

If you have any queries please contact tyler.mcinnes@otago.ac.nz