I am trying to create an integrated callset with coding regions from phased exomes and noncoding regions from a genotyping array. I would like to merge the data together in the correct phase. Since the exomes are already phased with read informed phasing, I don't want to rephase them because some of the phasing changes after doing this. Is there a way to statistically phase genetic data that has already been partially phased?
My data is in VCF format.