Heterozygous Variants On Male X/Y Chromosome (Exome Data)
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.
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Fatemeh Nabizadeh •
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See Pseudoautosomal region
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
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.
About HUWE1 gene,the depth of coverage for the alternative allele is 14x, while it is 35x for the ref allele.