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Y Chromosome Heterozygotes?

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.

variant-calling chromosome
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updated by Vitis Vitis • written by Hans • Hans

2 answers

Have a look at this wiki page:

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

Check to see if your hets are in these regions.

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written by Zev.Kronenberg Zev.Kronenberg

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

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written by Vivek Vivek

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.

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written by Hans • Hans

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.

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written by Vitis Vitis

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