“Variant Normalization”的版本间的差异
第9行: | 第9行: | ||
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. | 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 === | + | ==== 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: | 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: | ||
<pre> | <pre> | ||
A variant is parsimonious if and only if it is represented in as few nucleotides as possible an allele of length 0. | A variant is parsimonious if and only if it is represented in as few nucleotides as possible an allele of length 0. | ||
</pre> | </pre> |
2020年1月16日 (四) 05:11的版本
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.