Heterozygous Variants On Male X/Y Chromosome (Exome Data)

Question

[Fatemeh Nabizadeh]

Hello,

I am analyzing the Whole Exome Sequencing (WES) data of a male patient. When looking at the variants on X and Y chromosome, I find out many heterozygous variants.

I think they should all be hemizygous variants. Shouldn't they? What is the problem?

The variants were called using SamTools/GATK using hg19 reference genome.

[WouterDeCoster]

See Pseudoautosomal region

[Fatemeh Nabizadeh]

These are the two HET variants that seem not to be located in PARs:

ChrX 53566722 T>G

Gene name: HUWE1

ChrX 73811648 G>A

Gene name: RLIM

[WouterDeCoster]

What is the fraction of reads supporting the alternative allele? The second variant is in a segmental duplication, a fragment highly similar with a locus on chr15, so this could be a misalignment problem.

[Fatemeh Nabizadeh]

About HUWE1 gene,the depth of coverage for the alternative allele is 14x, while it is 35x for the ref allele.