cnvHap is a program for joint copy number genotyping, which uses a haplotype model of copy number variation and integrates data from multiple platforms. It also carries out CN association.
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Nat Methods. 2010 Jul;7(7):541-6. Epub 2010 May 30.
cnvHap: an integrative population and haplotype-based multiplatform model of SNPs and CNVs.
Coin LJ, Asher JE, Walters RG, Moustafa JS, de Smith AJ, Sladek R, Balding DJ, Froguel P, Blakemore AI.