Question: Genotype representation for male chromosome X and Y
0
gravatar for bioinforesearchquestions
2.1 years ago by
United States
bioinforesearchquestions160 wrote:

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?

genotype snps dnaseq vcf • 1.3k views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by bioinforesearchquestions160
0
gravatar for Devon Ryan
2.1 years ago by
Devon Ryan84k
Freiburg, Germany
Devon Ryan84k wrote:

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.

ADD COMMENTlink written 2.1 years ago by Devon Ryan84k
1

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.

ADD REPLYlink written 2.1 years ago by Len Trigg1.2k

Good to know, thanks for the info!

ADD REPLYlink written 2.1 years ago by Devon Ryan84k

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?

ADD REPLYlink written 2.1 years ago by bioinforesearchquestions160

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.

ADD REPLYlink written 2.1 years ago by Devon Ryan84k
1

Since OP is from a computer science background I would like point to the pseudo-autosomal regions on X/Y chromosomes: https://en.wikipedia.org/wiki/Pseudoautosomal_region

ADD REPLYlink written 2.1 years ago by WouterDeCoster32k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 672 users visited in the last hour