Hi, I have some unphased SNP (6 SNPs all from same gene) data from a human study, and know that some of these SNPs form a haplotype block (from Haploview). I now want to impute the genotypes of this block so that I can use them in other analyses.
In the past, I have used the Plink hap-phase command for this, which tabulates all possible hapltypes for each individual. These can then be exported for use in R or other programs.
However, the release notes of the latest Plink mentions that its haplotype phasing and imputation algorithms are obsolete! It recommend using BEAGLE for more accurate phasing.
However - I have not been able to find a way to impute all possible haplotypes for the individuals in my study using BEAGLE. The Plink output was very useful and produced all possible haplotypes for each individual and their posterior probability. My question is - is there a newer way to produce these same results without using Plink??