How to treat heterozygous GATK calls on haploid chromosomes (sex chrom in males)

Question

[QVINTVS_FABIVS_MAXIMVS]

How do people normally treat heterozygous HaplotypeCaller variants on haploid chromosomes, like sex chromosomes in males?

Do you usually omit such calls? Or is there a method to resolve the genotypes. I assume GATK is sophisticated enough that most of the true positive calls on these chromosomes would be outputted as homozygous genotypes.

[WouterDeCoster]

Don't forget the pseudoautosomal regions.

[QVINTVS_FABIVS_MAXIMVS]

Those should be treated as diploid, so heterozygous calls are fine.

Answer 1

[monicapenon]

How did you solve the issue of treating heterozygous variants in the X chromosome inside NON-pseudoautosomal regions for males?