Unified representation of genetic variants

被引：254

作者：

Tan, Adrian

Abecasis, Goncalo R.

Kang, Hyun Min ^{[1
]}

机构：

[1] Univ Michigan, Dept Biostat, Ann Arbor, MI 48109 USA

来源：

BIOINFORMATICS | 2015年 / 31卷 / 13期

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1093/bioinformatics/btv112

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

A genetic variant can be represented in the Variant Call Format (VCF) in multiple different ways. Inconsistent representation of variants between variant callers and analyses will magnify discrepancies between them and complicate variant filtering and duplicate removal. We present a software tool vt normalize that normalizes representation of genetic variants in the VCF. We formally define variant normalization as the consistent representation of genetic variants in an unambiguous and concise way and derive a simple general algorithm to enforce it. We demonstrate the inconsistent representation of variants across existing sequence analysis tools and show that our tool facilitates integration of diverse variant types and call sets.

引用

页码：2202 / 2204

页数：3

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