CNVnator is a tool for Copy number variation (CNV) discovery and genotyping from depth of read mapping.
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CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
Abyzov A, Urban AE, Snyder M, Gerstein M.
Genome Res. 2011 Jun;21(6):974-84. Epub 2011 Feb 7.