I have 3 sets of genotypes:
- A multiethnic panel of phased 1000G Phase 3 genotypes in IMPUTE2 format (.hap).
- Genotype likelihoods (GL) for 40 whole-genotypes of a population A in .vcf format (field FORMAT=GL)
- An array of about 600.000 SNP (30X coverage) from a population B, which is genetically close to A.
I'd like to impute the missing genotypes of B using phased genotypes from A as a reference population merged with the 1000G data. My problem is how to get phased genotypes from A given the genotype likelihood data, in order to merge them with the 1000G .hap data. I'd highly appreciate any suggestion on how to solve this or how to obtain good quality imputed genotypes from B. Many thanks.