R&D Seven Bridges Genomics, Cambridge, MA, USA.
R&D Totient, Cambridge, MA, USA.
Bioinformatics. 2018 Dec 15;34(24):4241-4247. doi: 10.1093/bioinformatics/bty443.
Several tools exist to count Mendelian violations in family trios by comparing variants at the same genomic positions. This naive variant comparison, however, fails to assess regions where multiple variants need to be examined together, resulting in reduced accuracy of existing Mendelian violation checking tools.
We introduce VBT, a trio concordance analysis tool, which identifies Mendelian violations by approximately solving the 3-way variant matching problem to resolve variant representation differences in family trios. We show that VBT outperforms previous trio comparison methods by accuracy.
VBT is implemented in C++ and source code is available under GNU GPLv3 license at the following URL: https://github.com/sbg/VBT-TrioAnalysis.git.
Supplementary data are available at Bioinformatics online.
有几种工具可以通过比较同一基因组位置的变异来计算孟德尔违规，从而对家族三人组进行计数。然而，这种简单的变异比较方法无法评估需要一起检查多个变异的区域，从而降低了现有孟德尔违规检查工具的准确性。
我们引入了 VBT，这是一种三人组一致性分析工具，它通过近似求解 3 -way 变体匹配问题来识别孟德尔违规，从而解决家族三人组中变体表示的差异。我们表明，VBT 的准确性优于以前的三人组比较方法。
VBT 是用 C++编写的，源代码可在以下网址以 GNU GPLv3 许可证获得：https://github.com/sbg/VBT-TrioAnalysis.git。
补充数据可在 Bioinformatics 在线获得。
