Genomic Visualization and Interpretations

Variant annotation and interpretation

When variants are identified in the genome (or transcriptome) some kind of annotation and need for interpretation invariably follows. There are many, many tools for annotation and interpretation in different contexts and for different purposes. In this section we explore just a few of these many options. First we will learn to use Ensembl’s Variant Effect Predictor (VEP), a popular and widely used variant transcript annotator. VEP has many functions, but it is first used to annotate variants in the context of set of known transcripts. The other resources we will use, ClinVar and CIViC attempt to summarize evidence for the clinical relevance of variants in inherited human diseases and cancer respectively.

Some here are some examples of variant annotation and interpretation contexts:

Module 5 Lecture