Variant Normalization

Introduction

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. A failure to recognize this will frequently result in inaccurate analyses.

On this wiki page, we describe a variant normalization procedure that is well defined for biallelic as well as multiallelic variants. We then provide a formal proof the procedure's correctness.

Definition

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.

Parsimony

In the context of variant representation, parsimony means representing a variant in as few nucleotides as possible without reducing the length of any allele to 0. It is a property describing the nature of the length of a variant's alleles and is defined as follows:

 A variant is parsimonious if and only if it is represented in as few nucleotides as possible an allele of length 0.