Through 23andMe, I have SNP genotypes from family members spanning three generations, incl. one parent and a sibling of the missing parent, multiple siblings in the middle generation, one child in the the third generation and the child's other parent, and some cousins. Some of these have around 500,000 markers, and some of them have around a million.
I want to phase these and infer the genotypes of the missing parent, and also use imputation to bring each individual as close to the million snps as reliably possible, using a combination of information contained within the pedigree and also data from sources like the 1000 Genomes Project. Do you have any advice on how to accomplish this or which programs if any would work?