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Genotype representation for male chromosome X and Y

Hi friends,

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?

snps dnaseq vcf genotype
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written by bioinforesearchquestions bioinforesearchquestions

Thanks, Devon. I have some samples for which I don't have the gender information.

I read somewhere that for male, there should be many mutations in chr Y and majority of the mutations in chr X should be homozygous alternate. Why it cant be heterozygous genotype?

Similarly, for female, they don't have Y chromosome. So there shouldn't be any mutations and mutations in chrX can be heterozygous and homozygous alternate.

Sorry, I am from computer science background. Can you explain it?

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written by bioinforesearchquestions bioinforesearchquestions

Please use ADD COMMENT when replying to an earlier reaction, as such this thread stays logically ordered and easy to follow.

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written by WouterDeCoster WouterDeCoster

1 answer

Variant callers don't know that you're sequencing an organism with haploid X/Y chromosomes in some but not all of your samples, so they treat everything as diploid. I've heard of many people skipping at least chromosome Y for this reason.

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written by Devon Ryan Devon Ryan

Thanks, Devon. I have some samples for which I don't have the gender information.

I read somewhere that for male, there should be many mutations in chr Y and majority of the mutations in chr X should be homozygous alternate. Why it cant be heterozygous genotype?

Similarly, for female, they don't have Y chromosome. So there shouldn't be any mutations and mutations in chrX can be heterozygous and homozygous alternate.

Sorry, I am from computer science background. Can you explain it?

• 1 views • link
written by bioinforesearchquestions bioinforesearchquestions

You should be able to tell just from chromosome X. The ones with higher numbers of heterozygous variants are female. For why, think of many each of X and Y males and females have.

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written by Devon Ryan Devon Ryan

That's not true of all variant callers. The RTG variant caller is sex-aware and will produce haploid GT where appropriate, according to the sex of the individuals as specified (including producing diploid calls for male within PAR regions).

RTG also includes a chrstats command which will help identify the sex for those samples where the sex is unknown.

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written by Len Trigg Len Trigg

Good to know, thanks for the info!

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written by Devon Ryan Devon Ryan

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