CNValidator: validating somatic copy-number inference.

Abstract

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. 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. CNValidator is available on GitHub at https://github.com/kuhnerlab/CNValidator. Supplementary data are available at Bioinformatics online.