The Variant Call Format (VCF) is a flexible file format specification that allows us to represent many different variant types ranging from SNPs, indels to copy number variations. However, variant representation in VCF is non-unique for variants that have explicitly expressed reference and alternate sequences.
On this wiki page, we describe a a variant classification system for VCF variants.
The normalization of a variant representation in VCF consists of two parts: parsimony and left alignment pertaining to the nature of a variant's length and position respectively.
This page is maintained by Adrian.