Five approaches to detect CNVs from NGS short reads. A. Paired-end mapping (PEM) strategy detects CNVs through discordantly mapped reads. A discordant mapping is produced if the distance between two ends of a read pair is significantly different from the average insert size. B. Split read (SR)-based methods use incompletely mapped read from each read pair to identify small CNVs. C. Read depth (RD)-based approach detects CNV by counting the number of reads mapped to each genomic region. In the figure, reads are mapped to three exome regions. D. Assembly (AS)-based approach detects CNVs by mapping contigs to the reference genome. E. Combinatorial approach combines RD and PEM information to detect CNVs.