The invention discloses an
annotation method and an
annotation system of whole-
genome variant data. The method comprises the following steps of S1, creating a variant
data file, wherein the variant data are stored according to a
national standard VCF format as an input file; S2, performing multi-
allele genotyping, firstly performing
genotype judgment, representing a basic group which is consistent with a
reference genome by zero, and representing the basic groups which are inconsistent with the
reference gene group by 1, 2, 3,..., then performing SNP and
InDel multi-
allele type resolution so that the
allele type is represented by zero and one; S3, causing
InDel generation position normalization, namely performing
InDel generation position normalization according to a left justification and simplification normalization method; and S4, performing
annotation, namely performing
gene structure annotation,
allele frequency annotation, variable site harm prediction and
pathogenicity annotation. The annotation method and the annotation
system improve integrity and accuracy of annotation information.