Variant: a “variant” is defined as a difference from the human reference genome sequence. A “heterozygote” (het) is a carrier of one copy of variant allele and one copy of reference allele, and a “homozygote” (hom) is a carrier of two copies of variant alleles. The “variant allele” is not necessarily the “minor” (as opposed to “major”) allele, or the “derived” (as opposed to “ancestral”) allele.
Sex chromosome variants:
female & chr Y & outside Pseudoautosomal Regions --> excluded
male & Het & (chr X or chr Y) & outside Pseudoautosomal Regions --> excluded
variants on sex chromosomes in pseudoautosomal regions are treated the same as variants on autosomes.