My question might be very trivial to others. I am working on VCF files. Recently I ended up in a confusion for the genotype representation in male X and Y chromosomes.
Human is a diploid organism, which is a well known fact. So we have following different genotypes for all autosomal chromosomes.
1) 0/0 - First allele is a reference base and second allele is a reference base (two alleles are present in two chromosomes)
2) 0/1 - First allele is a reference base and second allele is a alternate base (1 chr has ref base and its pair has alt base)
3) 1/1 - First allele is an alternate base and second allele is an alternate base (1 chr has alt base & its pair has alt base)
4) 1/2, 1/3, 1/4....so on
For male, chrX and chrY should have haploid calls. Then the genotype should be - GT : 0 instead of 0/0
GT : 1 instead of 1/1
GT : 2 instead of 1/2
But, why the VCFs are showing 0/1,1/1,1/2..etc similar to autosomal chromosomes?