I have two datasets one has genotype data for 30 SNPs and one has genotype data for 29 SNPs.I want to impute for the missing SNP and also want to determine the haplotype using these SNPs. This is how i am running the imputation in beagle
beagle.jar phased=file.phased unphased=test.unphased markers=markers missing=0 out=Result.
I get the imputed file as the result of this command but how do I get haplotype file? Ill appreciate any help.