Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone
Gustaf: Detecting and correctly classifying SVs in the NGS twilight zone
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DOI：
10.1093/bioinformatics/btu431
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发表时间：
2014-12-15
期刊：
影响因子：
5.8
通讯作者：
Reinert, Knut
中科院分区：
文献类型：
--
作者：
Trappe, Kathrin;Emde, Anne-Katrin;Reinert, Knut
动机：结构变异（SV）的景观，包括复杂的重复和易位模式是远远没有解决。SV检测工具通常表现出较低的协议，往往是面向某些类型或大小范围的变化和斗争，以正确分类的类型和确切大小的SVs.Results：我们提出古斯塔夫（通用mUlti-SpliT对齐），一个健全的通用多分裂SV检测工具，检测和分类缺失，倒位，分散的重复和易位>= 30 bp。我们的方法是基于一个通用的多分裂比对策略，可以确定SV断点与碱基对分辨率。我们表明Gustaf正确识别了SV，特别是在30到100 bp的范围内，我们称之为SV的下一代测序（NGS）模糊区，以及大于500 bp的更大的SV。Gustaf在我们的基准测试中比类似的工具表现得更好，并且还能够正确地识别分散的重复和易位的大小和位置，否则可能会被错误地分类，例如，大缺失。
Motivation: The landscape of structural variation (SV) including complex duplication and translocation patterns is far from resolved. SV detection tools usually exhibit low agreement, are often geared toward certain types or size ranges of variation and struggle to correctly classify the type and exact size of SVs.Results: We present Gustaf (Generic mUlti-SpliT Alignment Finder), a sound generic multi-split SV detection tool that detects and classifies deletions, inversions, dispersed duplications and translocations of >= 30 bp. Our approach is based on a generic multi-split alignment strategy that can identify SV breakpoints with base pair resolution. We show that Gustaf correctly identifies SVs, especially in the range from 30 to 100 bp, which we call the next-generation sequencing (NGS) twilight zone of SVs, as well as larger SVs > 500 bp. Gustaf performs better than similar tools in our benchmark and is furthermore able to correctly identify size and location of dispersed duplications and translocations, which otherwise might be wrongly classified, for example, as large deletions.