Annotation method and annotation system of whole-genome variant data

Abstract

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.

Description

technical field [0001] The present invention relates to the technical field of bioinformatics, in particular to an annotation method and annotation system for whole-genome variation data. Background technique [0002] With the development of sequencing technology and the reduction of cost, in the field of human health, human whole genome sequencing will surely become the mainstream trend in the future, and precision medicine will be the ultimate goal of sequencing. Accurately annotating the variation of the human genome is a necessary means to achieve precision medicine. [0003] The discovery of variant sites refers to the search for different base types at the same positions in the human individual genome and the human reference genome. These variant sites may be pathogenic sites that affect human health or cause human diseases. Based on the next-generation sequencing technology, the sequence obtained by sequencing is compared with the genome, and the difference bases bet...

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Problems solved by technology

[0008] Existing annotation tools such as Annovar developed and widely used by the Children's Hospital of Philadelphia in the United States provide gene structure annotations based on the above points; population mutation frequency annotations, but do not include frequencies of specific populations (such as Chinese populations); There are many software provided for value annotations, and there are no guiding annotation suggestions

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