trfermikit: a tool to discover VNTR-associated deletions.

We present trfermikit, a software tool designed to detect deletions larger than 50 bp occurring in Variable Number Tandem Repeats using Illumina DNA sequencing reads. In such regions, it achieves a better tradeoff between sensitivity and false discovery than a state-of-the-art structural variation caller, Manta and complements it by recovering a significant number of deletions that Manta missed. trfermikit is based upon the fermikit pipeline, which performs read assembly, maps the assembly to the reference genome and calls variants from the alignment. https://github.com/petermchale/trfermikit. Supplementary data are available at Bioinformatics online.

我们推出了trfermikit，这是一种软件工具，旨在利用Illumina DNA测序读数检测在可变数目串联重复序列中出现的大于50bp的缺失。在这类区域，它在灵敏度和错误发现率之间实现了比最先进的结构变异检测工具Manta更好的平衡，并通过恢复大量Manta遗漏的缺失来对其进行补充。trfermikit基于fermikit流程，该流程进行读段组装，将组装结果映射到参考基因组，并从比对结果中识别变异。https://github.com/petermchale/trfermikit。补充数据可在《生物信息学》在线获取。