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CNVphaser is a tool to infer alleles or haplotypes in copy number variable (CNV) genomic regions. The CNVphaser algorithm uses Partition-Ligation–Expectation-Maximization (PL-EM), and users may set three different initial value types. The algorithm can handle missing calls, any number of variant base types, and seed prior copies in the enumeration procedure of the EM algorithm. Note, an improved version, CNVphaserPro, is available. See links. (For noisy CNV data: MOCSphaser from the same research group).


DNA structural variation; Human genetics



Kato M, Nakamura Y, Tsunoda T "An algorithm for inferring complex haplotypes in a region of copy-number variation." Am J Hum Genet. 2008 Aug;83(2):157-69. Jul 17.
PMID: 18639202
PMCID: PMC2495074

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