Unified representation of genetic variants
Unified representation of genetic variants
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DOI：
10.1093/bioinformatics/btv112
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发表时间：
2015-07-01
期刊：
影响因子：
5.8
通讯作者：
Kang, Hyun Min
中科院分区：
文献类型：
--
作者：
Tan, Adrian;Abecasis, Goncalo R.;Kang, Hyun Min
遗传变异可以以多种不同的方式在变异调用格式（VCF）中表示。变体调用者和分析之间变体的不一致表示将放大它们之间的差异，并使变体过滤和重复删除复杂化。我们提出了一个软件工具vt normalize，规范化的遗传变异的VCF中的表示。我们正式定义变异规范化的一致表示的遗传变异的一个明确和简洁的方式，并推导出一个简单的通用算法来执行它。我们展示了现有的序列分析工具的变异不一致的表示，并表明我们的工具有利于不同的变异类型和调用集的整合。
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.