Relationship between query variants, reference annotation and sequence in the region of interest, and the complete reference genome/chromosome. For Ensembl genomes, the coordinate system is defined in 1-"residue"-based coordinates, from 1 to the length of the chromosome, L. The region of interest is a subset of the genome. The VariantClassifier uses a 0-"space"-based coordinate system to facilitate the description of indels. This local coordinate system ranges from 0 to the length of the reference sequence subregion, s. The reference annotation and query variants need to be specified in the region of interest's local coordinate system.
Li and Stockwell BMC Research Notes 2010 3:191 doi:10.1186/1756-0500-3-191