From Genome Analysis Wiki
→X Chromosome Imputation
=== 1. Split the X chromosome pedigree file by sex ===
# For females: follow the same protocol as for autosomes (phase with MaCH and impute with minimac).
# For males
## Convert the pedigree file into a MaCH haplotype file (missing genotypes should be encoded as: "0" or "." or "N" ) and impute using minimac as described above.
=== 2. Impute non-pseudo-autosomal part by sex ===
=== 3. Impute pseudo-autosomal part by sex ===
== Imputation quality evaluation ==