Loss of heterozygosity (LOH) happens when a heterozygous genome loses one of the two alleles at a locus. This may have an evolutionary advantage in highly unstable genomes such as those of hybrids (Smukowski Heil et al., 2017). By extracting LOH from a hybrid we understand which alleles were beneficial in its evolution. This is important in wild, clinical, and industrial settings (Gabaldón, 2020). The genomic properties of hybrids are still, however, poorly understood. LOH are studied with reliable short-read sequencing data (Mixão et al., 2019), but the downstream analysis is often done with custom scripts that reduce reproducibility and do not to leverage the power of a computing cluster. Here we present a program called “JLOH” that streamlines LOH extraction from sequencing data maximizing parallel computing.