PopDel is lightweight tool for calling and genotyping deletions (of a few hundred base-pairs and upwards) in short read paired-end data. Its main feature is the efficient processing of many samples in a single joint-calling process. Cohorts of 50,000 or more BAM-files are no problem for PopDel. It works by first creating a small insert-size profile of every BAM file. Then, in the calling step, all profiles are jointly processed to generate the deletion calls in a likelihood based approach and genotype every sample. The results are presented in standard VCF-4.2 format. PopDel is designed for short read paired end data of germline WGS data of diploid organisms (like human) only and is therefore unsuited for the analysis of WES data or somatic variants in cancer. PopDel's GitHub repository: https://github.com/kehrlab/PopDel