Department of Human Genetics and Utah Center for Genetic Discovery, University of Utah, Salt Lake City, UT 84112, USA.
Bioinformatics. 2022 Feb 7;38(5):1231-1234. doi: 10.1093/bioinformatics/btab805.
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.
我们介绍了 trfermikit，这是一款软件工具，旨在使用 Illumina DNA 测序reads 检测大于 50bp 的串联重复序列中的缺失。在这些区域，它在灵敏度和假阳性率之间实现了比最先进的结构变异调用者 Manta 更好的权衡，并且通过恢复大量 Manta 错过的缺失来补充它。trfermikit 基于 fermikit 管道，该管道执行读组装，将组装映射到参考基因组，并从对齐中调用变体。
https://github.com/petermchale/trfermikit。
补充数据可在 Bioinformatics 在线获得。
