Cancer genomes are frequently struck by chromosomal lesions. Next generation sequencing provides potentially high-resolution assays in a single analysis to detect copy number alterations (CNA). The implementation and usage of sequencing may partly be hampered by the lack of transparency in copy number calling algorithms. Here, we present the software CNAplot for aligned visualization of variant allele frequencies and read depth ratios generated from paired whole exome sequencing samples. We implement transparent statistics to evaluate shifts in allele frequencies and sequencing read counts in order to support a copy number event, to complement other tools and to detect somatic copy-neutral loss of heterozygosity.