See this article:

A tutorial on statistical methods for population association studies

https://www.comp.nus.edu.sg/~ksung/cs3225/materials/nrg1916.pdf

and search for "phased haplotype data rather than unphased genotypes"

Also see this post:

What Are Phased And Unphased Genotypes?

According to Larry, "Phased data are ordered along one chromosome and so from these data you know the haplotype. Unphased data are simply the genotypes without regard to which one of the pair of chromosomes holds that allele."

Use IMPUTE2:

"IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes".

https://mathgen.stats.ox.ac.uk/impute/impute_v2.html

or SNPator:

http://www.snpator.org/HelpManual/phasedld.htm See also this paper:

Linkage disequilibrium (LD) computation from phased data

http://rpackages.ianhowson.com/rforge/LDExplorer/man/ld.html