Phased vs Unphased Genotypes

http://www.nature.com/nrg/journal/v12/n10/full/nrg3054.html
phased haplotypes, which identify the alleles that are co-located on the same chromosome. Because sequence and SNP array data generally take the form of unphased genotypes, it is not directly observed which of the two parental chromosomes, or haplotypes, a particular allele falls on.

 
http://biostar.stackexchange.com/questions/7869/what-are-phased-and-unphased-genotypes

Phased data (use BEAGLE
(Browning and Browning 2007) ) are ordered along one chromosome and so from these data you know the haplotype (set of SNPs in a region). Unphased data are simply the genotypes without regard to which one of the pair of chromosomes holds that allele.  to identify paternally transmitted alleles

faculty.washington.edu/browning/beagle/beagle_3.3_12Feb11.pdf

parent-offspring trio

 If what you are studying are correlations between, say, pairs of SNPs, and can be influenced by recombination, like linkage disequilibrium or selective sweeps, then you need phased data.

http://www.biomedcentral.com/1471-2164/9/356

Single Nucleotide Polymorphism or SNP is a DNA sequence variation, occurring when a single nucleotide is altered [7].

 A SNP site that contains two different alleles is called biallelic, a SNP site that contains three different alleles is called triallelic and a SNP site that contains four different alleles is called tetraallelic.

Imputation has resulted in the detection of additional associations, particularly when combining data from multiple studies genotyped on different platforms