How To Know Sex Of A Pig By Viewing Bamfiles

Question

[Kwame]

Hello, I have bamfiles from some genes on the x-chromosomes for some individual animals but the sexes of the animals are not known. Is there a way I can determine the sexes by looking at read coverage in the bamfiles or by any other means? Thanks

[dfornika]

Which species are these 'animals?' Different species have different systems for sex determination.

[Kwame]

The animals are pigs

Answer 1

[JC]

If the specie sex definition is similar to human (only one pair of chromosomes define the sex type), the answer is yes, you can compare coverages in the sexual chromosomes to define it. Even in human there are some shared regions between X and Y, but a simple test looking for how many reads are mapped to each one and normalized by chromosome size can revel that.

[Sudeep]

I want to add that extreme precaution should be given since your animals are pigs, AFAIK even with the newest pig genome build (Sscrofa 10.2) the annotation on Y chromosome isn't that good

[JC]

you're right, now we know is pig. I will carefully select the regions to define an average coverage.

Answer 2

[Rm]

In short Difficult: for example: In canfam (dog) genome: Y chromosome is not present so it will not be possible to know.

Even if present : say in Human: there are lot of duplicate micro-regions between X, Y chromosomes: in my experience i have seen a lot of reads aligned to Y chromosome; when the samples were from females.

[JC]

For human I saw the same, but in females the average coverage for chrX is a the same level than the other chromosomes, the chrY is not completely covered and can be pointed from a male sample.

Answer 3

[Wen.Huang]

unless the animals are 100% inbred. it is possible to determine sex by counting heterozygous X sites. If they are mostly homo -> likely male; if a decent fraction is heterozygous -> likely female; This is how plink determine sex using genotypes.

[Kwame]

Thanks guys for your help

Answer 4

[Istvan Albert]

I recall Brent Pedersen posting this:

Given a set of samples with males and females, take only the data from the Y chromosome and do a PCA plot.

What are some less known yet simple and powerful bioinformatics data analysis steps that you commonly use

[JC]

really clever, but I think he plots only SNV data, isn't?

[Istvan Albert]

I put in a comment on that post asking for more info - hopefully Brent will visit soon and add more info

[brentp]

That plot was of expression data (or methylation, can't recall). You may be able to do the same by making rows of samples and columns of regions on the sex chromosomes with values of mean (or median) coverage. This would require you to have multiple samples and to know the sex of some of them.

[brentp]

that probably should be rows of regions and columns of samples...

[JC]

thanks for the details, some day I will need it