SUMMARY: 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. AVAILABILITY AND IMPLEMENTATION: https://github.com/petermchale/trfermikit. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.