Abstract
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.
© The Author(s) 2018. Published by Oxford University Press.
2018
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
