Handling of X-linked variants in males

[dconrad]

We currently model the ploidy of variants in the pseudoautosomal regions of the X chromosome the same as the non-PAR regions in males. Specifically, we treat all genotypes as homozygous. So if the male is het in the VCF (as may be the case in PAR, or due to mapping error of reads coming from the Y or elsewhere) we force the genotype to be homozygous for the alternate allele.