CNAplot, release version 1.2: OS X, Ubuntu, Windows

Cancer genomes are frequently struck by one or several chromosomal lesions. One group of these often extensive somatic structural variants are copy number alterations (CNA) of which gains or losses are the most common. Next generation sequencing provides potentially high-resolution assays which covers the coding or entire genome in a single analysis in a highly flexible manner. At least, such analyses are able to support the laboratory work-up and conclusions of the cytogeneticists and pathologists. In spite of the technological breakthroughs, experienced primarily in the last decade, the implementation and usage may partly be hampered by the lack of transparency in copy number calling algorithms and perhaps owing to its complexity. Here, we present CNAplot for aligned visualization of variant allele frequencies and read depth ratios generated from paired whole exome sequencing samples. We implement transparent statistical tests to evaluate shifts in allele frequencies and sequencing read counts in order to support a copy number event. This software may be used to complement other tools or techniques and to detect somatic copy neutral loss of heterozygosity, often referred to as aquired uniparental disomy.