I am unable to find these scores with the cohort browser in the UKB RAP.
The context:
With IGV, I have visualized the reads of a 2-bp insertion on chromosome X for a male. Strangely, this variant is heterozygous while you would expect a homozygous variant as the position of the variant is not in a pseudoautosomal region of chromosome X. The sex interference from the X and Y probe intensities gives a male sex, which is also reflected in the sex chromosome anueploidy variable. I am unable to find the X-chromosome heterozygosity scores in the cohort browser. Anyone aware whether/where this score is available? Or why it is not?
Alternatively, the variant might be located in a genomic regions that has been duplicated. Or if someone could think of another explanation why this male has a heterozygous call on the X-chromosome, I am happy to hear about it.
Thank you in advance!
Iris
As fas as I know, there is overall heterozygosity and ancestry corrected. If you want to calculate X chromosome heterozygosity I suggest following approach using array data , however, I did not tried it myself.
Using PLINK, extract only X chromosome markers
Using PLINK, compute homozygous counts using --het Alternatively you can export PLINK files to VCF using --recode and use vcftools --het
Compute heterozygosity using formula described here.
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As fas as I know, there is overall heterozygosity and ancestry corrected. If you want to calculate X chromosome heterozygosity I suggest following approach using array data , however, I did not tried it myself.
Thank you for you answer. Then I will calculate it myself.
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