AbstractMotivationThere are many tools for variant calling and effect prediction, but little to tie together large sample groups. Aggregating, sorting, and summarizing variants and effects across a cohort is often done withad hocscripts that must be re-written for every new project. In response, we have written MuCor, a tool to gather variants from a variety of input formats (including multiple files per sample), perform database lookups and frequency calculations, and write many report types. In addition to use in large studies with numerous samples, MuCor can also be employed to directly compare variant calls from the same sample across two or more platforms, parameters, or pipelines. A companion utility, DepthGauge, measures coverage at regions of interest to increase confidence in calls.AvailabilitySource code is freely available athttps://github.com/blachlylabContactjames.blachly@osumc.eduSupplementary dataSupplementary data, including detailed documentation, are available online.