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Revision as of 10:25, 5 September 2014
, 10:25, 5 September 2014→Definitions
= Definitions =
= Definitions =
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 definition of a variant is based on the definition of each allele with respect to the reference sequence. We consider 5 major types as follows.
;1. SNP
: The reference and alternate sequences are of length 1 and the base nucleotide is different from one another.
;2. MNP
: a.The reference and alternate sequences are of the same length and have to be greater than 1 and all nucleotides in the sequences differ from one another.
: OR
: b. all reference and alternate sequences have the same length.
;INDEL
: a. The reference and alternate sequence are not the same length.
: AND
: b. The removal of a subsequence of the longer sequence would reduce the longer sequence to the smaller sequence.
;CLUMPED
:
;SV
: The alternate sequence is represented by a angled bracket tag - <DEL>, for example.
= Example =
= Example =
