Research Environment Training Session: Finding participants based on genotypes

For many analyses, you may be starting with a (list of) gene(s) and you want to find all participants with variants in that/those gene(s). Or maybe you have variant loci and you want to get all participants with homo- or heterozygous alternative alleles at these loci.

In this training session, we will look at both point-and-click tools for finding variants and command line tools on the high-performance cluster (HPC), including using GEL-provided workflows.

We will have a look at the tiering tables that provide all variants that are considered to be plausibly pathogenic, and learn how to filter these by genes or loci. We will use the Integrated Variant Analysis tool (IVA) to search for variants by genes or loci, plus other parameters such as proband and parental genotypes, consequences and population frequencies. For each of these variants, we can pull out the participants with these variants. The training will also cover how you can use APIs to fetch the same data programmatically.

We will also use the Small Variant workflow and Structural Variant workflow that allow us to identify all variants in a list of genes, pulling out the platekeys of participants with these variants. To find individuals with variants at particular loci, we will use bcftools with the aggregated VCF files on the HPC.

You are only allowed to attend this session if you are eligible for data access. This means that you are a Research Network or Discovery Forum member that has met the necessary verification checks and passed our Information Governance training course. If you do not meet this criterion by 7th July 2025 you will be unregistered for this session.

Timetable

13.30 Introduction and admin
13.35 LabKey tables of variant genotypes

13.45 Finding genotypes with IVA

14.00 The Small Variant and Structural Variant workflows

14.15 Aggregated variant files

14.30 Using bcftools on the HPC
14.45 Getting help and questions

Learning objectives

After this training you will be able to:

• Know which tables which contain tiered variant data
• Use the IVA Variant Browser to filter variants.
• Differentiate between the Small Variant and Structural variant workflows and know when to use them.
• Understand the contents of the aggregated variant files: AggV2 and SomAgg.
• Run pipelines and tools on the GEL HPC and Cloud

Target audience

This training is aimed at researchers:

• working with the Genomics England Research Environment
• working with genetic and genomic variation data
• who can work on the command line to run tools and scripts