MOTIVATION: CNValidator assesses the quality of somatic copy-number calls based on coherency of haplotypes across multiple samples from the same individual. It is applicable to any copy-number calling algorithm, which makes calls independently for each sample. This test is useful in assessing the accuracy of copy-number calls, as well as choosing among alternative copy-number algorithms or tuning parameter values. RESULTS: On a dataset of somatic samples from individuals with Barrett's Esophagus, CNValidator provided feedback on the correctness of sample ploidy calls and also detected data quality issues. AVAILABILITY AND IMPLEMENTATION: CNValidator is available on GitHub at https://github.com/kuhnerlab/CNValidator. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.