I am using Arlequin and Chaplin software for generating haploypes, which require genotype data. Since males are hemizygous for X-chromosomes, how their haplotypes will be calculated in X-linked recessive disorder?
How to calculate haplotypes in males with X-linked recessive disorder.?
Of all people, I should not be the first to take on this question, espsecially as I have never worked with your software.
However, I would like to raise this concern. And maybe I will learn something here (nothing wrong with that, right?).
I always associated hemizygosity (not heterozygosity) with non-sequence differences from the + and - strands of a chromosome (like methyation differences). But I can certainly entertain the idea of hemizygous XY chromosomes.
I generally think of heterozygosity as differences beteween non-sex chromosomes (like SNP's).
Since your program most likely deals within the realm of better known heterozygous sequence changes (rather than relatively unconfirmed hemizygous changes), perhaps there is a communicaton gap between the (non-scientific) programmer and you.
Looking forward to other peoples feedback.
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