There are many interesting patterns that you can extract from genetic variant data. This can include patterns of linkage, balancing selection, or even inbreeding signals. One of the most common approaches is to find sites on the genome that are under selection.
This in-person workshop introduces the basics of genetic selection analysis. It will step you through the process of identifying signals of selection using your own data (or an example genomic dataset) using the outlier analysis method.
This workshop covers the same material as our online Genetic Outlier Analysis workshop held in February but will focus on the analysis of participants’ own data. Past participants are welcome to apply. Preference will be given to those who have their own data they can bring to the workshop.
Lead Trainer: Dr Katarina Stuart, Research Fellow, University of Auckland.
Date/Time: 4 - 5 July 2024, 10am - 4:30pm AEST
Location: Room 102, Mathews Building, F23 Library Walk, University of New South Wales, Kensington, NSW (no virtual option available).
Format:
This in-person workshop will take place over two sessions. You must attend both sessions as they build on one another. Expert trainers will introduce new topics and guide you through hands-on activities to help you put your new skills into action.
Learning outcomes:
By the end of the workshop you should be able to:
Download example genomic data (or prepare your own)
Use the PCAdapt tool to identify outlier loci within a genome.
Use VCFtools to identify outlier SNPs in pairwise population comparisons.
Use Bayescan and Baypass to identify outlier SNPs based on allele frequencies across multiple populations.
Use Baypass to identify SNPs that are related to phenotype (GWAS)
Compare the results of the different methods and discuss the results.
Who the workshop is for:
This workshop is for researchers associated with an Australian organisation and/or members of the Genetics Society of AustralAsia who will use genetic selection analysis as part of their projects.
Preference will be given to those who have their own data they can bring to the workshop.
Past participants are welcome to apply.
This workshop requires you to have:
(Preferred) Your own data variant files in VCF format and a tab delimited sample metadata file containing individual ID and other important info for your samples.
Some familiarity with biological concepts, including the concept of selection.
Basic command line (bash) knowledge. You must know how to navigate the directory structure and copy files between the computers. If you need a refresher on Unix/Linux try this online tutorial.
Basic knowledge of R. You must know how to set up directories, run commands, reading in and outputting files. If you need a refresher on R try the Introduction to R and RStudio section of this online tutorial.
How to apply:
This workshop is free but participation is subject to application with selection.
Applications close at 11:59pm AEST, Wednesday 19 June 2024.
Applications will be reviewed by the organising committee and all applicants will be informed of the status of their application (successful, waiting list, unsuccessful) after the closing date. More information on the selection process is provided in our advice on applying for Australian BioCommons workshops.
This workshop is presented by the Australian BioCommons and the Genetics Society of AustralAsia with the assistance of a network of facilitators from the national Bioinformatics Training Cooperative.
This event is part of a series of bioinformatics training events. If you'd like to hear when registrations open for other events, please subscribe to Australian BioCommons.