ABSTRACT
This chapter explains the basics of the Human Gene Variation Society (HGVS) nomenclature, and then shows how it is used to describe the various classes of variant that are encountered in WES and WGS data. The HGVS Website about the mutation nomenclature is very useful for learning about the HGVS standard. The chapter provides a high-level review by introducing the HGVS standard for describing each of the variant types that can be annotated by Jannovar. Jannovar can be used to annotate the variants in a Variant Call Format (VCF) file. It is important to use a transcript description file that matches the genome build being analyzed: the coordinates of genes change on ma jor genome build version changes (e.g., from GRCh37 to GRCh38) as single bases or whole segments are added to or removed from a chromosome. Jannovar will add the variant type and a representative annotation to each line of the VCF file.
