Variant analysis

Variants can be analysed in different ways. For example, you might want to determine which genes the variants hit and what effects they have on them. Tools such as the Ensembl VEP and SnpEff can be used for this. You may wish to filter or merge your VCF file, which you can do with VCF Tools.

Have a look at our webinar to learn more about Ensembl VEP.

Having filtered your data and identified interesting genes or variants, you can explore them further using databases such as:

We will see some examples of this in the case studies in part II of this course.

You may also wish to explore the variant consequences and any associated predictions. This can be useful for understanding why a particular variant may cause a particular phenotype. When studying a number of variants to determine which is causal for a phenotype, predictions can be helpful for prioritising variants for further study.

However, prediction can never be as valuable as experimental data. Any predictions determined bioinformatically should be followed up experimentally, and no conclusions should be drawn in what variant causes a phenotype based only on bioinformatic predictions.

Now let’s take a quick look at some ways of predicting and visualising the effect of variation on protein structure and function.