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vcf2diploid is a tool for personal genome constructor. It can be used to construct a personal diploid genome sequence by including personal variants into reference genome.

Rozowsky J, Abyzov A, Wang J, Alves P, Raha D, Harmanci A, Leng J, Bjornson R, Kong Y, Kitabayashi N, Bhardwaj N, Rubin M, Snyder M, Gerstein M. AlleleSeq: Analysis of Allele-Specific Expression and Binding in a Network Framework. (Mol Syst Biol. 2011 Aug 2;7:522.