Y Chromosome Heterozygotes?

Question

[Hans]

I called variants in my Y chromosome with Samtools mpileup. Quite a number of heterozygotes were reported; after phasing they were mostly 0|1. Who can explain me this strange fact.

Answer 1

[Zev.Kronenberg]

Have a look at this wiki page:

http://en.wikipedia.org/wiki/Pseudoautosomal_region

Check to see if your hets are in these regions.

[Vivek]

To add to this I'd also check the mapping qualities for those regions, since most of them could also be mis-mapped reads.

[Hans]

The HET calls were in the non-PAR region. The mis-mapping could be a reason as the 'variants' came mostly in pairs in pair-end reads. I will now try UnifiedGenotyper from GATK to see if there is a difference.

Answer 2

[Vitis]

If pseudoautomsomal regions and repetitive regions/mapping qualities have been ruled out, one other possibility is copy number variations. If multiple copies of the same sequences with different individual bases in the middle, the reads from multiple copies would pile up at the same regions and the difference between copies would resemble heterozygous variants. There are ample examples of these in genomes of inbreeding plants. I wouldn't not be surprised if it happens on Y chromosomes.